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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Disrupted NOS2 metabolism drives myoblast response to wasting-associated cytokines

Highlights: • Amino acid metabolism is impacted in myoblasts treated with cancer cell conditioned media. • Inflammatory cytokines induce nitric oxide synthase 2 in myoblasts. • Elevated nitric oxide synthase 2 activity impairs myoblast proliferation and differentiation. Skeletal muscle wasting drives negative clinical outcomes and is associated with a spectrum of pathologies including cancer. Cancer cachexia is a multi-factorial syndrome that encompasses skeletal muscle wasting and remains understudied, despite being a frequent and serious co-morbidity. Deviation from the homeostatic balance between breakdown and regeneration leads to muscle wasting disorders, such as cancer cachexia. Muscle stem cells (MuSCs) are the cellular compartment responsible for muscle regeneration, which makes MuSCs an intriguing target in the context of wasting muscle. Molecular studies investigating MuSCs and skeletal muscle wasting largely focus on transcriptional changes, but our group and others propose that metabolic changes are another layer of cellular regulation underlying MuSC dysfunction in cancer cachexia. In the present study, we combined gene expression and non-targeted metabolomic profiling of myoblasts exposed to wasting conditions (cancer cell conditioned media, CC-CM) to derive a more complete picture of the myoblast response to wasting factors. After mapping these features to annotated pathways, we found that more than half of the mapped pathways were amino acid-related, linking global amino acid metabolic disruption to conditioned media-induced myoblast defects. Notably, arginine metabolism was a highly enriched pathway in combined metabolomic and transcriptomic data. Arginine catabolism generates nitric oxide (NO), an important signaling molecule known to have negative effects on mature muscle. We hypothesize that tumor-derived disruptions in Nitric Oxide Synthase (NOS)2-regulated arginine catabolism impair differentiation of MuSCs. The work presented here further investigates the effect of NOS2 overactivity on myoblast proliferation and differentiation. We show that NOS2 inhibition is sufficient to rescue wasting phenotypes associated with inflammatory cytokines. Ultimately, this work provides new insights into MuSC biology and opens up potential therapeutic avenues for addressing disrupted MuSC dynamics in cancer cachexia.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13 C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Neural network ensembles and uncertainty estimation for predictions of inelastic mechanical deformation using a finite element method-neural network approach

The finite element method (FEM) is widely used to simulate a variety of physics phenomena. Approaches that integrate FEM with neural networks (NNs) are typically leveraged as an alternative to conducting expensive FEM simulations in order to reduce the computational cost without significantly sacrificing accuracy. However, these methods can produce biased predictions that deviate from those obtained with FEM, since these hybrid FEM-NN approaches rely on approximations trained using physically relevant quantities. In this work, an uncertainty estimation framework is introduced that leverages ensembles of Bayesian neural networks to produce diverse sets of predictions using a hybrid FEM-NN approach that approximates internal forces on a deforming solid body. The uncertainty estimator developed herein reliably infers upper bounds of bias/variance in the predictions for a wide range of interpolation and extrapolation cases using a three-element FEM-NN model of a bar undergoing plastic deformation. This proposed framework offers a powerful tool for assessing the reliability of physics-based surrogate models by establishing uncertainty estimates for predictions spanning a wide range of possible load cases.

42 ENGINEERING↗
DOE OSTI2025

Active control of laser beam pointing for the Zettawatt-Equivalent Ultrashort pulse laser System: a proof-of-principle study with 16-inch optics

We present a proof-of-principle study of active beam-pointing control for the Zettawatt-Equivalent Ultrashort pulse laser System (ZEUS) using a piezo-actuated 16-inch mirror. To the best of our knowledge, this is the largest actively controlled mirror reported in a high-power laser system. A simple proportional feedback control was implemented based on a field-programmable gate array, which reduced the standard deviation of beam-pointing fluctuations by 91% to 0.075 μrad in the horizontal direction and by 78% to 0.25 μrad in the vertical direction. We also demonstrated the elimination of long-term pointing jitter caused by temperature drift using the same apparatus.

laser pointing control↗
DOE OSTI2022

Computing the viscous effect in early-time drop impact dynamics

The impact of a liquid drop on a solid surface involves many intertwined physical effects, and is influenced by drop velocity, surface tension, ambient pressure and liquid viscosity, among others. Experiments by Kolinski et al. ( Phys. Rev. Lett. , vol. 112, no. 13, 2014 b , p. 134501) show that the liquid–air interface begins to deviate away from the solid surface even before contact. They found that the lift-off of the interface starts at a critical time that scales with the square root of the kinematic viscosity of the liquid. To understand this, we study the approach of a liquid drop towards a solid surface in the presence of an intervening gas layer. We take a numerical approach to solve the Navier–Stokes equations for the liquid, coupled to the compressible lubrication equations for the gas, in two dimensions. With this approach, we recover the experimentally captured early time effect of liquid viscosity on the drop impact, but our results show that lift-off time and liquid kinematic viscosity have a more complex dependence than the square-root scaling relationship. We also predict the effect of interfacial tension at the liquid–gas interface on the drop impact, showing that it mediates the lift-off behaviour.

42 ENGINEERING↗
DOE OSTI2023

Statistical characterization of a shock interacting with an inclined gas column

We present a statistical characterization of the interaction between a planar shock and a finite-diameter, cylindrical column of dense gas based on three-dimensional, large-eddy simulation results. In the simulation, the column of gas is initially inclined at an angle $\alpha _0$ with respect to the shock plane. Effects of the initial column angle on the mixing characteristics are examined at Mach number 2.0 for column incline angles $1^\circ$ , $5^\circ$ , $10^\circ$ and $30^\circ$ . Mean velocity profiles show that the column angle affects the gas velocity components in the vertical plane, but not in the spanwise direction. The gas undergoes higher initial upward acceleration at larger initial column incline angles. With time, the gas motion tends to become one-dimensional in the streamwise direction. Initially, velocity fluctuations are most intense within the interior of the column, but concentrate near the column leading edge over time. At high wavenumbers $\kappa$ , the turbulent kinetic energy spectra follow a power-law scaling of $\kappa ^{-1}$ . The structure functions of the mass fraction do not clearly demonstrate power-law scaling except at early times for $\alpha _0=30^\circ$ , manifesting overall trends very similar to those observed in earlier experiments. Probability distributions of the mass fraction show independence of the mean and the standard deviation of the mixed gas on $\alpha _0$ . The column angle was also found to have little effect on the mixing efficiency characterized by the molecular mixedness. Velocity components in the streamwise and transverse directions tend towards a bimodal distribution for larger $\alpha _{0}$ .

42 ENGINEERING↗
DOE OSTI2022

Measures of quasisymmetry for stellarators

Quasisymmetric stellarators are an attractive class of optimised magnetic confinement configurations. The property of quasisymmetry (QS) is in practice limited to be approximate, and thus the construction requires measures that quantify the deviation from the exact property. In this paper we study three measure candidates used in the literature, placing the focus on their origin and a comparison of their forms. The analysis shows clearly the lack of universality in these measures. As these metrics do not directly correspond to any physical property (except when exactly quasisymmetric), optimisation should employ additional physical metrics for guidance. It is suggested that close to QS minima, one should treat QS metrics through inequality constraints so that additional physics metrics dominate optimisation. The impact of different quasisymmetric measures on optimisation is presented through an example, for which the standard metric that weights the asymmetric Fourier modes of the field magnitude appears to perform best.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Finite orbit width effects in large aspect ratio stellarators

New orbit-averaged equations for low collisionality neoclassical fluxes in large aspect ratio stellarators with mirror ratios close to unity are derived. The equations retain finite orbit width effects by employing the second adiabatic invariant $J$ as a velocity-space coordinate and they have been implemented in the orbit-averaged neoclassical code KNOSOS (Velasco et al. , J. Comput. Phys. , vol. 418, 2020, 109512; Velasco et al. , Nucl. Fusion , vol. 61, 2021, 116013). The equations are used to study the $1/\nu$ regime and the lower collisionality regimes. For generic large aspect ratio stellarators with mirror ratios close to unity, as the collision frequency decreases, the $1/\nu$ regime transitions directly into the $\nu$ regime, without passing through a $\sqrt {\nu }$ regime. An explicit formula for the neoclassical fluxes in the $\nu$ regime is obtained. The formula includes the effect of particles that transition between different types of wells. While these transitions produce stochastic scattering independent of the value of the collision frequency in velocity space, the diffusion in real space remains proportional to the collision frequency. The $\sqrt {\nu }$ regime is only recovered in large aspect ratio stellarators close to omnigeneity: large aspect ratio stellarators with large mirror ratios and optimized large aspect ratio stellarators with mirror ratios close to unity. Neoclassical transport in large aspect ratio stellarators with large mirror ratios can be calculated with the orbit-averaged equations derived by Calvo et al. ( Plasma Phys. Control. Fusion , vol. 59, 2017, 055014). In these stellarators, the $\sqrt {\nu }$ regime exists in the collisionality interval $(a/R) \ln (R/a) \ll \nu _{ii} R a/\rho _i v_{ti} \ll R/a$ . In optimized large aspect ratio stellarators with mirror ratios close to unity, the $\sqrt {\nu }$ regime occurs in an interval of collisionality that depends on the deviation from omnigeneity $\delta$ : $\delta ^{2} |\ln \delta | \ll \nu _{ii} R a/\rho _i v_{ti} \ll 1$ . Here, $\nu _{ii}$ is the ion–ion collision frequency, $\rho _i$ and $v_{ti}$ are the ion gyroradius and thermal speed, and $a$ and $R$ are the minor and major radii.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Fast-ion transport in quasisymmetric equilibria in the presence of a resonant Alfvénic perturbation

Significant progress has been made in designing magnetic fields that provide excellent confinement of the guiding-centre trajectories of alpha particles using quasisymmetry (QS). Given the reduction in this transport channel, we assess the impact of resonant Alfvén eigenmodes (AEs) on the guiding-centre motion. The AE amplitudes are chosen to be consistent with experimental measurements and large-scale simulations. We evaluate the drift resonance condition, phase-space island width and island overlap criterion for quasisymmetric configurations. Kinetic Poincaré plots elucidate features of the transport, including stiff transport above a critical perturbation amplitude. Our analysis highlights key departures from the AE-driven transport in tokamaks, such as the avoidance of phase-space island overlap in quasihelical configurations and the enhanced transport due to wide phase-space islands in low magnetic shear configurations. In configurations that are closer to QS, with QS deviations $\delta B/B_0 \lesssim 10^{-3}$ , the transport is primarily driven by the AE, while configurations that are further from QS, $\delta B/B_0 \sim 10^{-2}$ , experience significant transport due to the QS-breaking fields in addition to the AE.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Kinetic stability of Chapman–Enskog plasmas

In this paper, we investigate the kinetic stability of classical, collisional plasma – that is, plasma in which the mean-free-path $\lambda$ of constituent particles is short compared with the length scale $L$ over which fields and bulk motions in the plasma vary macroscopically, and the collision time is short compared with the evolution time. Fluid equations are typically used to describe such plasmas, since their distribution functions are close to being Maxwellian. The small deviations from the Maxwellian distribution are calculated via the Chapman–Enskog (CE) expansion in $\lambda /L \ll 1$ , and determine macroscopic momentum and heat fluxes in the plasma. Such a calculation is only valid if the underlying CE distribution function is stable at collisionless length scales and/or time scales. We find that at sufficiently high plasma $\beta$ , the CE distribution function can be subject to numerous microinstabilities across a wide range of scales. For a particular form of the CE distribution function arising in strongly magnetised plasma ( viz. plasma in which the Larmor periods of particles are much smaller than collision times), we provide a detailed analytic characterisation of all significant microinstabilities, including peak growth rates and their associated wavenumbers. Of specific note is the discovery of several new microinstabilities, including one at sub-electron-Larmor scales (the ‘whisper instability’) whose growth rate in certain parameter regimes is large compared with other instabilities. Our approach enables us to construct the kinetic stability maps of classical, two-species collisional plasma in terms of $\lambda$ , the electron inertial scale $d_e$ and the plasma $\beta$ . This work is of general consequence in emphasising the fact that high- $\beta$ collisional plasmas can be kinetically unstable; for strongly magnetised CE plasmas, the condition for instability is $\beta \gtrsim L/\lambda$ . In this situation, the determination of transport coefficients via the standard CE approach is not valid.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Self-organization in collisionless, high- β turbulence

The magnetohydrodynamic (MHD) equations, as a collisional fluid model that remains in local thermodynamic equilibrium (LTE), have long been used to describe turbulence in myriad space and astrophysical plasmas. Yet, the vast majority of these plasmas, from the solar wind to the intracluster medium (ICM) of galaxy clusters, are only weakly collisional at best, meaning that significant deviations from LTE are not only possible but common. Recent studies have demonstrated that the kinetic physics inherent to this weakly collisional regime can fundamentally transform the evolution of such plasmas across a wide range of scales. Here, we explore the consequences of pressure anisotropy and Larmor-scale instabilities for collisionless, β $\gg$ 1, turbulence, focusing on the role of a self-organizational effect known as ‘magneto-immutability’. We describe this self-organization analytically through a high-β, reduced ordering of the Chew–Goldberger–Low-MHD (CGL-MHD) equations, finding that it is a robust inertial-range effect that dynamically suppresses magnetic-field-strength fluctuations, anisotropic-pressure stresses and dissipation due to heat fluxes. As a result, the turbulent cascade of Alfvénic fluctuations continues below the putative viscous scale to form a robust, nearly conservative, MHD-like inertial range. These findings are confirmed numerically via Landau-fluid CGL-MHD turbulence simulations that employ a collisional closure to mimic the effects of microinstabilities. We find that microinstabilities occupy a small (~5%) volume-filling fraction of the plasma, even when the pressure anisotropy is driven strongly towards its instability thresholds. We discuss these results in the context of recent predictions for ion-vs-electron heating in low-luminosity accretion flows and observations implying suppressed viscosity in ICM turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Lectures on statistical mechanics

Presented here is a transcription of the lecture notes from Professor Allan N. Kaufman’s graduate statistical mechanics course Physics 212A and 212B at the University of California Berkeley from the 1972–1973 academic year. 212A addressed equilibrium statistical mechanics with topics: fundamentals (micro-canonical and sub-canonical ensembles, adiabatic law and action conservation, fluctuations, pressure, and virial theorem), classical fluids and other systems (equation of state, deviations from ideality, virial coefficients and van der Waals potential, canonical ensemble and partition function, quasistatic evolution, grand-canonical ensemble and partition function, chemical potential, simple model of a phase transition, quantum virial expansion, numerical simulation of equations of state, and phase transition), chemical equilibrium (systems with multiple species and chemical reactions, law of mass action, Saha equation, chemical equilibrium including ionization and excited states), and long-range interactions (including Coulomb, dipole, and gravitational interactions, Debye–Hückel theory, and shielding). 212B addressed nonequilibrium statistical mechanics with topics: fundamentals (definitions: realizations, moments, characteristic function, and discrete variables), Brownian motion (Langevin equation, fluctuation–dissipation theorem, spatial diffusion, Boltzmann’s H-theorem), Liouville and Klimontovich equations, Landau equation (derivation, elaboration, and H-theorem, and irreversibility), Markov processes and Fokker–Planck equation (derivations of the Fokker–Planck equation and a master equation), linear response and transport theory (linear Boltzmann equation, linear response theory of Kubo and Mori, relation of entropy production to electrical conductivity, transport relations and coefficients, normal mode solutions of the transport equations, sketch of a generalized Langevin equation method for transport theory), and an introduction to nonequilibrium quantum statistical mechanics.

plasma dynamics↗
DOE OSTI2025

Bootstrap current modeling in M3D-C1

Bootstrap current plays a crucial role in the equilibrium of magnetically confined plasmas, particularly in quasi-symmetric stellarators and in tokamaks, where it can represent bulk of the electric current density. Accurate modeling of this current is essential for understanding the magnetohydrodynamic (MHD) equilibrium and stability of these configurations. This study expands the modeling capabilities of M3D-C1, an extended-MHD code, by implementing self-consistent physics models for bootstrap current. It employs two analytical frameworks: a generalized Sauter model (Sauter et al. 1999 Phys. Plasmas vol. 6, no. 7, pp. 2834–2839), and a revised Sauter-like model (Redl et al. 2021 Phys. Plasmas vol. 28, no. 2, pp. 022502). The isomorphism described by Landreman et al. (2022 Phys. Rev. Lett. vol. 128, pp. 035001) is employed to apply these models to quasi-symmetric stellarators. The implementation in M3D-C1 is benchmarked against neoclassical codes, including NEO, XGCa and SFINCS, showing excellent agreement. These improvements allow M3D-C1 to self-consistently calculate the neoclassical contributions to plasma current in axisymmetric and quasi-symmetric configurations, providing a more accurate representation of the plasma behavior in these configurations. A workflow for evaluating the neoclassical transport using SFINCS with arbitrary toroidal equilibria calculated using M3D-C1 is also presented. This workflow enables a quantitative evaluation of the error in the Sauter-like model in cases that deviate from axi- or quasi-symmetry (e.g. through the development of an MHD instability).

fusion plasma↗
DOE OSTI2024

Distinct evolutionary lineages of Schistocephalus parasites infecting co-occurring sculpin and stickleback fishes in Alaska

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [S.D.] = 15) and stickleback (mean = 86; S.D. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Analysis of Interpretable Data Representations for 4D-STEM Using Unsupervised Learning

Abstract Understanding the structure of materials is crucial for engineering devices and materials with enhanced performance. Four-dimensional scanning transmission electron microscopy (4D-STEM) is capable of mapping nanometer-scale local crystallographic structure over micron-scale field of views. However, 4D-STEM datasets can contain tens of thousands of images from a wide variety of material structures, making it difficult to automate detection and classification of structures. Traditional automated analysis pipelines for 4D-STEM focus on supervised approaches, which require prior knowledge of the material structure and cannot describe anomalous or deviant structures. In this article, a pipeline for engineering 4D-STEM feature representations for unsupervised clustering using non-negative matrix factorization (NMF) is introduced. Each feature is evaluated using NMF and results are presented for both simulated and experimental data. It is shown that some data representations more reliably identify overlapping grains. Additionally, real space refinement is applied to identify spatially distinct sample regions, allowing for size and shape analysis to be performed. This work lays the foundation for improved analysis of nanoscale structural features in materials that deviate from expected crystallographic arrangement using 4D-STEM.

Bruefach, Alexandra (ORCID:0000000209323477)↗
DOE OSTI2021

Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.

Nielson, Felicity F.↗
DOE OSTI2021

Resolving Severe Elemental Isobaric Interferences with a Combined Atomic and Molecular Ionization Source - Orbitrap Mass Spectrometry Approach: The 87Sr and 87Rb Geochronology Pair

Many fields of basic and applied sciences, including geochronology, astronomy, metabolism, nutrition and forensics rely on the ability of mass spectrometry to make isotope ratio measurements with a high degree of certainty. The inability to resolve difficult isobaric interferences still plagues certain measurements of this type. A combined atomic and molecular (CAM) ionization source has been interfaced to a high-field Orbitrap mass spectrometer in an effort to alleviate severe atomic, isobaric interferences. Specifically, this work examines the geochronological-significant 87Sr and 87Rb isotope pair. The mass difference between 87Sr and 87Rb is ~0.3 mDa, requiring a minimum resolving power (R = m/?m) of ~290,000, a value ~30X higher than available with conventional (sector-field) elemental mass spectrometers. Under ultra-high resolution conditions, Sr isotope ratio accuracy and precision were evaluated using NIST Sr SRM 987, yielding precision values of <0.1% relative standard deviation (RSD) for the major isotopes and a calculated LOD of 2 pg mL-1, equivalent to 120 fg Sr for a 60 µL injection. In addition to manipulating the signal transient length, which controls the Orbitrap resolving power, the total number of ions in the electrostatic trap and the relative ion populations (i.e. the 87Sr/87Rb concentration ratio), were found to be influential towards resolving the isobaric species. Ultimately, the 87Sr and 87Rb isotopes were baseline resolved with a calculated mass resolution of >1.7 M. At equal 87Sr and 87Rb intensities, the 87Sr/86Sr was measured as 0.71294 (an error of 0.37%) with a precision of 0.097 %RSD, clearly reflecting the alleviation of the isobaric interference.

Hoegg, Edward D.↗
DOE OSTI2025

Data Set Analysis to Reduce Uncertainty in Formula Assignments of Ultrahigh Resolution Mass Spectra

Environmental samples contain a vast array of organic compounds with diverse elemental compositions and heteroatom content. Molecular formula assignments of ultrahigh resolution mass spectra (HRMS) hold promise for elucidating the molecular composition of these compounds. However, the need to account for an assortment of heteroatoms increases the uncertainty associated with individual assignments – and ultimately the ecological, biological, and biogeochemical insights gleaned from the assignments. To address this challenge, we introduce a formula assignment strategy that leverages HRMS data sets to improve assignment confidence, filter false assignments, and mitigate bias in assignment routines. The strategy, implemented using CoreMS, first identifies the highest confidence assignment for a recurring ion in a data set by assessing the mass accuracy and isotopologue similarity of all assignments to the ion across the data set. The second component of the strategy examines the consistency of mass errors for an assigned ion throughout a data set and flags formulas with statistically unlikely deviations in mass error. Here, we illustrate the application and utility of the strategy by comparing its results against documented misassignment patterns within a set of oceanographic samples that were measured with 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Because the efficacy of our strategy improves with data set size, it is particularly useful for enhancing assignment confidence in large HRMS data sets common in studies of environmental systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗