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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

10 Be at iThemba LABS using a silicon nitride membrane stack as absorber for isobar suppression

10 Be is an important isotope for accelerator mass spectrometry (AMS) because of the demand for cosmogenic radionuclide dating methods in the earth science and paleo-sciences community. At the iThemba Laboratory for Accelerator Based Science (iThemba LABS) we implemented full suppression of the interfering isobar 10 B using a silicon nitride foil-stack, utilizing the 2+ charge state for high efficiency. We demonstrate the performance of this newly established AMS system using standards and test samples. Here we further present the results of an inter-comparison between iThemba LABS and the Center for Accelerator Mass Spectrometry/Lawrence Livermore National Laboratory, on AMS samples prepared from purified quartz at the University of Vermont. The results for 10 Be from the laboratories are in close agreement, fully consistent with cross-calibration between them. AMS results for 26 Al are in similarly good agreement, demonstrating the performance and accuracy of iThemba LABS for the most commonly measured in situ produced cosmogenic nuclides.

10-Be↗
DOE OSTI2023

Applying the core-satellite species concept: Characteristics of rare and common riverine dissolved organic matter

Introduction: Dissolved organic matter (DOM) composition varies over space and time, with a multitude of factors driving the presence or absence of each compound found in the complex DOM mixture. Compounds ubiquitously present across a wide range of river systems (hereafter termed core compounds) may differ in chemical composition and reactivity from compounds present in only a few settings (hereafter termed satellite compounds). Here, we investigated the spatial patterns in DOM molecular formulae presence (occupancy) in surface water and sediments across 97 river corridors at a continental scale using the “Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems—WHONDRS” research consortium. Methods: We used a novel data-driven approach to identify core and satellite compounds and compared their molecular properties identified with Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Results: In this work, we found that core compounds clustered around intermediate hydrogen/carbon and oxygen/carbon ratios across both sediment and surface water samples, whereas the satellite compounds varied widely in their elemental composition. Within surface water samples, core compounds were dominated by lignin-like formulae, whereas protein-like formulae dominated the core pool in sediment samples. In contrast, satellite molecular formulae were more evenly distributed between compound classes in both sediment and water molecules. Core compounds found in both sediment and water exhibited lower molecular mass, lower oxidation state, and a higher degree of aromaticity, and were inferred to be more persistent than global satellite compounds. Higher putative biochemical transformations were found in core than satellite compounds, suggesting that the core pool was more processed. Discussion: The observed differences in chemical properties of core and satellite compounds point to potential differences in their sources and contribution to DOM processing in river corridors. Overall, our work points to the potential of data-driven approaches separating rare and common compounds to reduce some of the complexity inherent in studying riverine DOM.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter

Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it is a significant contributor for determining signal-to-noise ratios and MS resolution. Here we report on the integration of a 2 GS/s, 14-bit ADC with a structures for lossless ion manipulations (SLIM)-IMS-MS and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided an effective reduction in digitized noise by factor of ~6, owing largely to the use of smaller bit sizes. The low baseline allowed the threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without causing overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a complex mixture of heavy labeled phosphopeptides showed that the 14-bit ADC (compared to the 8-bit ADC) provided a modest signal-to-noise increase (~1.5 to 2-fold) for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernable signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ~14-fold fewer mass spectra to be averaged to produce a mass spectrum with similar S/N as the 8-bit ADC under identical conditions, potentially providing an order of magnitude higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra, and allows a much fuller picture of analyte profiles in complex mixtures to be acquired.

data acquisition, digitization, ion mobility spect↗
DOE OSTI2023

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells

T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.

mass spectrometry↗
DOE OSTI2024

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Analytical advances to study the air – water interfacial chemistry in the atmosphere

Formation of aqueous secondary organic aerosol (aqSOA) at the air – liquid interface recently has attracted a lot of attention in atmospheric chemistry. The discrepancies in mass distributions, aerosol oxidative capacity, liquid water content, hygroscopic growth of aerosols, and formation of clouds and fogs suggest that interfacial chemistry play a more important role than previously deemed. However, detailed mechanisms at the air–water interface remain unclear owing to the lack of comprehensive understanding that underpins complicated interfacial phenomena, which are not easily measurable from field campaigns, laboratory measurements, or computational simulations. Here, this review highlights relevant and recent technical advancement employed to study aqSOA encompassing spectroscopy and mass spectrometry. The current knowledge on the aqSOA processes is digested with an emphasis on recent research of interfacial aqSOA formation including laboratory studies and model simulations. Finally, future directions of the interfacial chemistry are recommended for field and laboratory studies as well as theoretical efforts to resolve interfacial challenges in atmospheric chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Surfactant inhibition mechanisms of carbonate mineral dissolution in shale

Surfactants are common additives to hydraulic fracturing and enhanced oil recovery (EOR) fluids, and are under consideration for amendment to supercritical carbon dioxide for geological carbon sequestration (GCS). The effect of a common anionic surfactant, internal olefin sulfonate (IOS), on mineral dissolution from shale into brine was evaluated. When added to brine at concentrations exceeding the critical micelle concentration (94 mg/L), IOS inhibited carbonate mineral dissolution in an Eagle Ford shale, as well as dissolution of optical quality calcite (the dominant carbonate in the shale). Laser profilometry images provide spatial resolution across > 3 orders of magnitude, and indicate that IOS addition to brine both enhances the formation of new etch pits in calcite, and impedes their further growth. Time-of-flight secondary ion mass spectrometry surface profiles show for the first time that IOS preferentially adsorbs at calcite pit edges versus flat calcite surfaces (i.e., terraces). Surface pressure calculations, sulfur K-edge near edge X-ray absorption fine structure (NEXAFS) spectroscopy results, and density functional theory (DFT) calculations support this observation; the DFT results indicate that the sulfonate head group of the IOS molecule binds strongly to the calcite step site as compared to the terrace site. The S K-edge NEXAFS results indicate that IOS adsorbed more to etched calcite surfaces compared to smooth calcite surfaces. Overall, the results indicate that weak adsorption on flat calcite surfaces (i.e., terraces) disrupts water structure and enhances mass transfer of dissolution, while strong adsorption on calcite pit edges displaces adsorbed water and inhibits further etch pit growth. This work provides the first direct evidence of preferential adsorption of IOS to etched calcite surfaces and links it to macroscopic dissolution kinetics. Finally, this work has implications for surfactant-containing fluids used in hydraulic fracturing, EOR and potentially GCS for subsurface injection into carbonate rich reservoirs.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Investigation of the Mechanisms Underpinning Plasma-Catalyst Interaction for the Conversion of Methane to Oxygenates

Plasma catalysis is a promising approach to further enhance the conversion of methane into value-added products such as methanol. In this work, the mechanisms enabling the conversion of methane to CO, CO 2 and methanol enabled by plasma-enhanced catalysis were investigated. A catalyst reactor was incorporated downstream of the plasma jet to enable the separation between plasma generation and the catalyst bed. An enhancement in CH 3 OH and CO 2 production was observed for the shortest distance between the plasma and catalyst compared to the plasma-only case. Plasma-enabled gas heating was shown not to be responsible for the observed synergy while a gas temperature increase as low as 30-40 K significantly impacted desorption rates of CH 3 OH/C 2 H 5 OH on alumina particles. Correlations between molecular beam mass spectrometry (MBMS) measurements at the inlet and outlet of the catalytic reactor suggest that the observed synergistic effect was caused by radical species most likely the CH 3 O 2 radical. As a result, this study shows that surface reactions induced by radicals such as alkylperoxy radicals might play an important role in surface reactions in plasma-catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Solution characterization of the dynamic conjugative entry exclusion protein TraG

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor–donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding–mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Inhibition of atomic layer deposition of TiO 2 by functionalizing silicon surface with 4-fluorophenylboronic acid

As the size of the components in electronic devices decreases, new approaches and chemical modification schemes are needed to produce nanometer-size features with bottom-up manufacturing. Organic monolayers can be used as effective resists to block the growth of materials on non-growth substrates in area-selective deposition methods. However, choosing the appropriate surface modification requires knowledge of the corresponding chemistry and also a detailed investigation of the behavior of the functionalized surface in realistic deposition schemes. This study aims to investigate the chemistry of boronic acids that can be used to prepare such non-growth areas on elemental semiconductors. 4-Fluorophenylboronic acid is used as a model to investigate the possibility to utilize the Si(100) surface functionalized with this compound as a non-growth substrate in a titanium dioxide (TiO 2 ) deposition scheme based on sequential doses of tetrakis(dimethylamido)titanium and water. Here, a combination of X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry allows for a better understanding of the process. The resulting surface is shown to be an effective non-growth area to TiO 2 deposition when compared to currently used H-terminated silicon surfaces but to exhibit much higher stability in ambient conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Pyrolysis_Molecular_Beam_Mass_Spectra_for_Standard_Biomass_Samples_and_Natural_Variants_of_Switchgrass_Grown_Under_Different_Conditions

This data consists of total ion chromatogram (TIC) normalized Pyrolysis-Molecular Beam Mass Spectrometry (py-MBMS) spectra collected to predict lignin content and lignin monomeric ratios for “Variation in Biomass Yield and Cell Wall Composition in Switchgrass Natural Variants Under Two Nitrogen Regimes” (https://doi.org/10.1007/s12155-025-10838-8).

09 BIOMASS FUELS↗
DOE OSTI2025

High Spatial Resolution Mapping of Retained Fission Gas

Fission gas isotopic analysis provides quantitative high precision determination of irradiated nuclear fuel burnup, offers diagnostic value, and informs fuel performance models. A measurement capability has been developed at Idaho National Laboratory (INL) for the release of retained fission gas using a focused laser and static noble gas mass spectrometry (MS) analysis. This high resolution (10s microns spot size) capability was demonstrated using Xe implanted metal foils.

07 - ISOTOPES AND RADIATION SOURCES↗
DOE OSTI2021

Optical and mass-spectral characterization of mixed-gas flowing atmospheric-pressure afterglow sources

Plasma-based ambient desorption/ionization (ADI) sources for mass spectrometry (MS) often use helium as the primary discharge gas due to the large reaction cross section of excited helium species with atmospheric gases, which ultimately leads to efficient reagent-ion formation. However, some studies have shown that mixed-gas plasmas provide unique advantages. For instance, our group showed that a helium-oxygen flowing atmospheric-pressure afterglow (He:O 2 -FAPA) source yielded enhanced ion signals for small polar analytes, but compounds with aromatic rings underwent chemical modification to produce pyrylium species. Here, it is shown that the addition of H 2 to the helium FAPA gas significantly decreased the reagent-ion signals, but analyte-ion signal was not affected to the same degree. In addition, mass spectra obtained with He:H 2 -FAPA were chemically cleaner with fewer ions stemming from analyte species and produced less oxidation of analytes. Addition of nitrogen increased the abundance of negative reagent ions (e.g., NO 2 - and NO 3 - ) which led to enhanced ion signal for RDX. To better understand these unique advantages of a mixed-gas FAPA, the impact of molecular-gas (O 2 , N 2 , or H 2 ) addition on the optical-emission spectra from the discharge was also measured. Spatially resolved emission was obtained from the anode- and negative-glow regions. In general, addition of small fractions (~0.1%) of molecular gases decreased helium and OH emission intensities. Atomic oxygen and hydrogen emission increased with the addition of O 2 and H 2 , respectively. Furthermore, emission characteristics of N 2 , N 2 + , and NO with respect to molecular gas composition on He-FAPA were measured. Finally, fundamental plasma parameters, such as OH rotational temperature (T rot ), were also calculated for these mixed-gas systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

ToF-SIMS imaging reveals that p -hydroxybenzoate groups specifically decorate the lignin of fibres in the xylem of poplar and willow

Esterified phenolics occur as γ-linked lignin acylations in many plant taxa but little is known about the distribution or function of such groups. In the family Salicaceae, p-hydroxybenzoate groups are present in the lignin of poplars (Populus spp.) and willows (Salix spp.). In this study, the distribution of cell wall-bound p-hydroxybenzoate was examined in different tissue and cell types of poplar and willow trees. This analysis showed that p-hydroxybenzoate groups were most prevalent in juvenile stems, and were elevated in tension wood and following nitrogen fertilisation. Closer examination of stem cross-sections using time-of-flight secondary-ion mass spectrometry (ToF-SIMS) directly showed that p-hydroxybenzoate groups occur predominantly in the cell walls of fibres and are largely absent from vessel elements. Furthermore, these results point to a role for ester-linked groups in modifying the syringyl-rich lignin of fibres, perhaps to strengthen the cell walls of these structural elements or to increase lignification rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Practical considerations for amino acid isotope analysis

Over the last few decades, isotopic analysis of amino acids at the compound- and position-specific levels has been rapidly advancing across diverse fields. As these techniques progress, evaluation of isotopic fractionation associated with sample workup is essential. This critical review of analytical methods through the lens of isotope geochemistry provides a benchmark for researchers across disciplines seeking to make compound- and position-specific amino acid isotope measurements. We focus on preparation, acid hydrolysis, clean-up, derivatization, separation, and C, H, N, and S isotope measurement. Despite substantial customizability across these steps, the following general recommendations should maximize recovery while minimizing isotopic fractionation. Samples should be freeze-dried and stored anoxically at ≤ –20 °C prior to conventional acid hydrolysis (6N HCl, 110 °C, 20–24 h, anoxic), which suffices for many residues. Both gas and liquid chromatographic (GC and LC, respectively) techniques are well-established and separate about 15 amino acids; LC bypasses the need for derivatization, while GC provides higher sensitivity. Furthermore, when derivatization is needed, n-acetyl and alkoxycarbonyl esters provide the most reproducible C isotope ratios. For compound-specific analyses, online GC–IRMS and LC–IRMS systems offer the easiest workflow, but EA–IRMS enables potential multi-element isotope analysis. Emerging techniques like high-resolution mass spectrometry are also promising for multi-element analysis and recover position-specific isotopic information. Looking forward to the next decade of innovation, isotope geochemists and ecologists can improve amino acid isotope analysis by focusing on streamlining multi-element analysis and standardizing calibration practices across laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Identifying Candidate Biomarkers of Ionizing Radiation in Human Pulmonary Microvascular Lumens Using Microfluidics—A Pilot Study

The microvasculature system is critical for the delivery and removal of key nutrients and waste products and is significantly damaged by ionizing radiation. Single-cell capillaries and microvasculature structures are the primary cause of circulatory dysfunction, one that results in morbidities leading to progressive tissue and organ failure and premature death. Identifying tissue-specific biomarkers that are predictive of the extent of tissue and organ damage will aid in developing medical countermeasures for treating individuals exposed to ionizing radiation. In this pilot study, we developed and tested a 17 µL human-derived microvascular microfluidic lumen for identifying candidate biomarkers of ionizing radiation exposure. Through mass-spectrometry-based proteomics, we detected 35 proteins that may be candidate early biomarkers of ionizing radiation exposure. This pilot study demonstrates the feasibility of using humanized microfluidic and organ-on-a-chip systems for biomarker discovery studies. A more elaborate study of sufficient statistical power is needed to identify candidate biomarkers and test medical countermeasures of ionizing radiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling

Nanoliter liquid handling capabilities in bioanalytical workflows can reduce reagent costs and improve sample processing efficiency. Here we report the successful modification of a low-cost commercially available pipetting robot, the Opentrons 1 (OT1), using inexpensive 3D-printed parts to accommodate low-nanoliter volumes. The pipetting accuracy and precision of the modified OT1 for 50 nL volumes of water was 0.2% and 2%, respectively. The accuracy and precision at 20 nL was 1% and 3.8%, respectively. The platform was successfully applied to the preparation of low-nanogram proteomic samples for liquid chromatography-mass spectrometry analysis. The modified OT1 is thus an effective platform for nanoliter liquid handling and, at a total cost of less than $6000 including the commercial liquid handler and all modifications, is far less expensive and more versatile than other platforms with similar capabilities, placing this technology within reach of a far broader scientific community.

47 OTHER INSTRUMENTATION↗