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At least 1,585 records · Page 88

In situ study on heavy ion irradiation induced microstructure evolution in single crystal Cu with nanovoids at elevated temperature

Understanding the response of nanovoids to irradiation damage advances our capability to design radiation tolerant materials. Recent in situ studies reveal the shrinkage of hexagon-shaped nanovoids in (110) textured Cu. However, the evolution of voids with irregular geometries under irradiation is less well understood. Here, in situ Kr ion irradiation was performed at 100 °C on single-crystal Cu (112) that possesses nanovoids with high aspect ratio. In situ studies show these elongated voids fragment into smaller voids and shrink gradually with increasing dose. Phase field simulations confirm that fragmentation of the void is governed by the competing kinetics between atoms diffusing toward and away from the elongated nanovoid. In conclusion, cost irradiation analysis reveals the formation of high-density defect clusters.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Compilation and Evaluation of Isomeric Fission Yield Ratios

Fission yields are essential data for reactor physics, forensics, and astrophysics. In some cases, the fission yield of a fragment is divided between the ground state and a long-lived excited state, and the relative population of the two states is referred to as the isomeric ratio. In this work, we present a comprehensive compilation of experimental isomeric fission yield ratios for all target and projectile combinations. When possible, these data are combined to provide recommended isomeric fission yield ratios for low energy neutron-induced fission and spontaneous fission. The recommended ratios are compared to the traditional Madland-England model, which attempts to describe the isomeric ratios with a single parameter relating to the angular momentum of the fragment. It is found that the model does not reliably reproduce isomeric ratios outside the few nuclei it was fitted to, and its simplified treatment of the statistical process following population in fission results in average spin values, which are neither constant nor follow a recently observed saw-tooth pattern.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The cyclotron gas stopper at FRIB getting ready for operations

Linear gas stopping cells have been used for nearly two decades to slow down projectile fragments at the National Superconducting Cyclotron Laboratory, now the Facility for Rare Isotope Beams, for experiments with low-energy and reaccelerated beams. In order to efficiently stop and rapidly extract light to medium-mass fast ions, a cyclotron gas-stopper has been constructed. It uses a cyclotron-type magnet and a helium-gas filled stopping chamber to slow down the injected beam. RF ion guides transport the stopped ions to the center of the magnet and axially through the bore before acceleration to <60 keV. Following successful offline tests, the cyclotron stopper was moved to an experimental vault and connected to a new momentum–compression beam line. Beam transport to and into the cyclotron stopper was tested with stable beams. Finally, using 46 K fragments, the first successful stopping and extraction of a high-energy beam with the cyclotron stopper was demonstrated.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Design of a separate effects MiniFuel irradiation experiment investigating microstructure evolution in high burnup UO 2

The microstructural evolution of UO 2 fuel pellets during commercial operation in light water reactors (LWRs) is known to vary significantly across the pellet radius due to spatial variations in local temperature and burnup. The primary obstacle to extending LWR refueling cycles to 24-month intervals is the susceptibility of certain high burnup fuel microstructures to fuel fragmentation, relocation, and dispersal (FFRD) during a loss of coolant accident (LOCA). Although FFRD of the high burnup structure in the rim region of a pellet is well studied, the fine fragmentation that has been observed in a second region, near the midradius of the pellet (termed the “dark zone”) following mock LOCA testing of high burnup commercial fuel rods is less understood. This paper describes the design, analysis, and execution of a separate effects MiniFuel irradiation experiment that aims to identify the specific temperature and burnup regimes under which FFRD-susceptible dark zone microstructures form. The small disc specimens (3 mm diameter by ∼0.3 mm thick) enable more precise control of the relatively uniform temperature and burnup conditions. A total of 42 specimens were fabricated with typical LWR fuel densities (∼96%–98% of theoretical density) and grain sizes (∼12 μm) and are being irradiated over a range of temperatures (600°C–1000°C) and discharge burnups (50–72 MWd/kg-U) that bound the midradius region of high burnup LWR fuel. Fuel specimens with identical 235 U enrichments were inserted in two irradiation locations in the High Flux Isotope Reactor and are currently undergoing irradiation to further evaluate the impact of rate effects (fission rate, time at temperature) on the microstructural evolution. The fuel fabrication and the thermal and neutronic simulations used for designing the experiment are detailed in this paper. A secondary objective of the experiment is to observe fission gas release (FGR) under the various irradiation conditions, and this work provides first-order predictions of FGR from all fuel specimens. The insights gained from these experiments will inform future high burnup core designs that could minimize the formation of susceptible microstructures and ultimately enable 24-month refueling cycles while minimizing the fraction of the fuel susceptible to FFRD.

FFRD↗

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗

Transverse Λ polarization in e + e - collisions

In this paper we study transverse polarization of hyperons in single-inclusive leptonic annihilation. We show that when the transverse momentum of the baryon is measured with respect to the thrust axis, a transverse momentum dependent (TMD) factorization formalism is required and the polarization is generated by the TMD polarizing fragmentation function (TMD PFF), D 1 T &#x22A5; . However, when the transverse momentum of the baryon is measured with respect to the momentum of the initial leptons, a collinear twist-3 formalism is required and the polarization is generated by the intrinsic collinear twist-3 fragmentation function D T . Thus while these measurements differ from one another only by a change in the measurement axis, they probe different distribution functions. Recently, Belle measured a significant polarization in single-inclusive baryon production as a function of the transverse momentum with respect to the thrust axis. However, this data can in principle be re-analyzed to measure the polarization as a function of the transverse momentum of the baryon with respect to the lepton pair. This observable could be the first significant probe of the function, D T . In this paper, we first develop a TMD formalism for polarization; we then present a recent twist-3 formalism that was established to describe polarization. Using the TMD formalism, we demonstrate that the polarization at OPAL and Belle can be described using the twist-2 TMD factorization formalism. Finally, we make a theoretical prediction for this polarization in the collinear twist-3 formalism at Belle.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Collins function for pion-in-jet production in polarized pp collisions: a test of universality and factorization

We present an updated study of the Collins azimuthal asymmetries for pion-in-jet production in polarized pp collisions. To this aim, we employ a recent extraction of the transversity and Collins fragmentation functions from semi-inclusive deep inelastic scattering and e + e - annihilation into hadron pairs processes, obtained within a simplified transverse momentum dependent (TMD) approach at leading order in the strong coupling constant α s . In the present case we adopt a collinear configuration for the initial state, keeping transverse momentum effects only in the fragmentation mechanism. Our theoretical estimates, when compared against 200 GeV and 510 GeV data from the STAR Collaboration, show a generally good agreement for the distributions in the transverse momentum of the jet, the pion longitudinal momentum fraction and its transverse momentum with respect to the jet direction. While not being a proof, due the assumptions and limitations behind the entire approach, these findings corroborate the hypothesis of TMD factorization for such processes as well as of the universality of the Collins function and, once again, of a reduced impact of the proper TMD evolution on azimuthal asymmetries. We will also present predictions based on an extraction of the Collins and transversity distributions where information from data on single spin asymmetry for inclusive pion production in p ↑ p collisions is included through a Bayesian reweighting procedure.

Azimuthal asymmetries↗

Post-detonation fireball thermometry via femtosecond-picosecond coherent anti-Stokes Raman Scattering (CARS)

Accurate knowledge of post-detonation fireball temperatures is important for understanding device performance and for validation of numerical models. Such measurements are difficult to make even under controlled laboratory conditions. Here, temperature measurements were performed in the fireball of a commercial detonator (RP-80, Teledyne RISI). The explosion and fragments were contained in a plastic enclosure with glass windows for optical access. A hybrid femtosecond-picosecond (fs-ps) rotational coherent anti-Stokes Raman scattering (CARS) instrument was used to perform gas-phase thermometry along a one-dimensional measurement volume in a single laser shot. The 13-mm-thick windows on the explosive-containment housing introduced significant nonlinear chirp on the fs lasers pulses, which reduced the Raman excitation bandwidth and did not allow for efficient excitation of high-J Raman transitions populated at flame temperatures. To overcome this, distinct pump and Stokes pulses were used in conjunction with spectral focusing, achieved by varying the relative timing between the pump and Stokes pulses to preferentially excite Raman transitions relevant to flame thermometry. Light scattering from particulate matter and solid fragments was a significant challenge and was mitigated using a new polarization scheme to isolate the CARS signal. Fireball temperatures were measured 35–40 mm above the detonator, 12–25 mm radially outward from the detonator centerline, and at 18 and 28 µs after initiation. At these locations and times, significant mixing between the detonation products and ambient air had occurred thus increasing the nitrogen-based CARS thermometry signal. Initial measurements show a distribution of fireball temperatures in the range 300–2000 K with higher temperatures occurring 28 µs after detonation.

42 ENGINEERING↗

On the prediction of pressure effects for the combination kinetics of two alkyl radicals with the geometric mean rule

Here, alkyl combination reactions, along with their reverse alkane unimolecular decomposition reactions, are widely present in pyrolysis and combustion systems. These reactions occur mainly at temperatures at which their rate coefficients depend on pressure, and only a few studies have explored this dependence for large size alkyls. The accurate calculation of these kinetic data is limited by the size of the alkyl fragments involved, since the theoretical methods used are computationally expensive. Therefore, little reliable data is available for the modeling of real fuels alkane decomposition kinetics. In this paper, we propose an alternative approach that allows an accurate estimation of pressure-dependent kinetic rates for the combination of long-chain alkyl radicals, based on tabulated reaction models. The rates of combination of linear alkyls radicals forming ethane to pentane were calculated using the CASPT2-F12/cc-pVDZ-F12 level within VRC-TST theory combined with master-equation simulations. The computed high-pressure limit rate coefficients showed that n-propyl could be a minimum-size representative structure for larger n-alkyl chain, but this approach fails to capture the pressure dependence of the reaction that remains size-dependent for larger alkyls. The Geometric Mean Rule (GMR), a simple rule that links the self and cross-reactions of three alkyl radicals, is used to address this issue. Our theoretical calculations show for the first time that the GMR applies not only at the high-pressure limit, but also for every pressure explored. The GMR is shown to be accurate, with a maximum 22 % deviation in the falloff region for the estimation of rates for small alkyl combinations. Using this method, we propose a tabulated reaction rate rule for the combination of alkyl radicals up to C5+C5. The use of computed rate coefficients with the GMR approximation opens ways to develop pressure-dependent reaction rate rules for large n-alkyl combinations, based on accurate and computationally expensive theoretical calculations on smaller alkyl fragments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ToF-SIMS spectral analysis of Shewanella oneidensis MR-1 biofilms

Analysis of bacterial biofilms is particularly challenging and important with diverse applications from systems biology to biotechnology. Among the variety of techniques that have been applied, time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many powerful features in studying the surface characteristics of biofilms. ToF-SIMS offers high spatial resolution, mass resolution, and mass accuracy, which permit surface sensitive analysis of biofilm components. Thus, ToF-SIMS provides a powerful solution to addressing the challenge of bacterial biofilm analysis. This dataset covers ToF-SIMS analysis of Shewanella oneidensis MR-1 isolated from freshwater lake sediment in New York state. The MR-1 strain is known to have metal and sulfur reducing properties and it can be used for bioremediation and wastewater treatment. There is a current need to identify small molecules and fragments produced from bacterial biofilms, especially those from extracellular polymeric substance (EPS). Static ToF-SIMS spectra of MR-1 were obtained using an IONTOF TOF.SIMS V instrument equipped with a 25 keV Bi$^+_3$ metal ion gun. Identified molecules and molecular fragments are compared against known biological databases and the reported peaks have at least 65 ppm mass accuracy. These molecules range from lipids, fatty acids, flavonoids, and quinolones to other naturally occurring organic compounds. It is anticipated that the mass spectral identification of key peaks will assist detection of metabolites, EPS molecules like polysaccharides, and biologically relevant small organic molecules using ToF-SIMS in future surface and interface research.

59 BASIC BIOLOGICAL SCIENCES↗

U-Pu and Ba-Cs isotopic measurements on Trinitite by laser ablation sampling on the Neoma MC-ICP-MS

In this study we present the results of combined U-Pu and Ba-Cs isotope measurements obtained by laser ablation (LA) sampling of two glassy debris fragments (‘Trinitite’) from the world's first atomic bomb detonation conducted in New Mexico on July 16, 1945. Our primary goal in conducting these measurements was to understand whether examination of the U-Pu and Ba-Cs systematics by direct sampling (e.g. without any chemical separation or purification prior to isotope ratio measurement) could yield meaningful information that would differentiate the Trinitite fragments from glassy material lacking a nuclear fission signature. These measurements were conducted on a ThermoFisher Scientific Neoma multi collector – inductively coupled plasma – mass spectrometer (MC-ICP-MS), which is a relatively new MC-ICP-MS platform, so we also examine the behavior of these isotope systems in standards sampled in solution and via LA. Unsurprisingly, the measurements made on purified solutions of the U, Pu, and Ba isotopic standards produce high precision isotope ratios. Furthermore, this extends to the U-Pu measurements made by LA sampling, with the expected degradation in precision and accuracy related to matrix effects and signal intensity fluctuation. However, the Ba-Cs data acquired by LA is of low precision across all of the matrices examined and bears evidence of complex mass fractionation that will require further investigation to resolve. In total, our results indicate that the observed U-Pu isotope data are of sufficient quality to accurately constrain the U and Pu isotopic composition of glass containing sub-ppm levels of these elements which in turn could be used to differentiate glass containing anthropogenic fission products from natural glass whereas the Ba-Cs LA data cannot be used for this purpose until further methodological refinement is performed.

Ba-Cs↗

Sixty days of head-down tilt bed rest with or without artificial gravity do not affect the neuromuscular secretome

Highlights: • Long-term bed rest with/without artificial gravity does not affect the neuromuscular secretome. • Serum concentrations of markers of muscle wasting are not affected by bed rest/artificial gravity. • C-terminal Agrin Fragment serum concentrations are not affected by bed rest/artificial gravity. • Human centrifugation during bed rest does not have a negative impact on the neuromuscular secretome. Artificial gravity is a potential countermeasure to attenuate effects of weightlessness during long-term spaceflight, including losses of muscle mass and function, possibly to some extent attributable to disturbed neuromuscular interaction. The 60-day AGBRESA bed-rest study was conducted with 24 participants (16 men, 8 women; 33 ± 9 years; 175 ± 9 cm; 74 ± 10 kg; 8 control group, 8 continuous (cAG) and 8 intermittent (iAG) centrifugation) to assess the impact of bed rest with or without daily 30-min continuous/intermittent centrifugation with 1G at the centre of mass. Fasting blood samples were collected before and on day 6, 20, 40 and 57 during 6° head-down tilt bed rest. Concentrations of circulating markers of muscle wasting (GDF-8/myostatin; slow skeletal muscle troponin T; prostaglandin E2), neurotrophic factors (BDNF; GDNF) and C-terminal Agrin Fragment (CAF) were determined by ELISAs. Creatine kinase activity was assessed by colorimetric enzyme assay. Repeated-measures ANOVAs were conducted with TIME as within-subject, and INTERVENTION and SEX as between-subject factors. The analyses revealed no significant effect of bed rest or sex on any of the parameters. Continuous or intermittent artificial gravity is a safe intervention that does not have a negative impact of the neuromuscular secretome.

60 APPLIED LIFE SCIENCES↗

Hyperglycemia alters mitochondrial respiration efficiency and mitophagy in human podocytes

Highlights: • Impairment of mitochondrial dynamics underlies the pathogenesis of type 2 diabetes. • Mitochondrial respiration is altered in glomeruli isolated from diabetic STZ-rats. • High glucose induces mitochondrial fission and fragmentation in human podocytes. • Mitochondrial fusion, biogenesis and mitophagy are reduced in HG-treated podocytes. • HG can injure the kidney by alteration of podocytes and glomerular bioenergetics. Podocytes constitute the outer layer of the renal glomerular filtration barrier. Their energy requirements strongly depend on efficient oxidative respiration, which is tightly connected with mitochondrial dynamics. We hypothesized that hyperglycemia modulates energy metabolism in glomeruli and podocytes and contributes to the development of diabetic kidney disease. We found that oxygen consumption rates were severely reduced in glomeruli from diabetic rats and in human podocytes that were cultured in high glucose concentration (30 mM; HG). In these models, all of the mitochondrial respiratory parameters, including basal and maximal respiration, ATP production, and spare respiratory capacity, were significantly decreased. Podocytes that were treated with HG showed a fragmented mitochondrial network, together with a decrease in expression of the mitochondrial fusion markers MFN1, MFN2, and OPA1, and an increase in the activity of the fission marker DRP1. We showed that markers of mitochondrial biogenesis, such as PGC-1α and TFAM, decreased in HG-treated podocytes. Moreover, PINK1/parkin-dependent mitophagy was inhibited in these cells. These results provide evidence that hyperglycemia impairs mitochondrial dynamics and turnover, which may underlie the remarkable deterioration of mitochondrial respiration parameters in glomeruli and podocytes.

60 APPLIED LIFE SCIENCES↗

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity

Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a Buffer Modification Workflow (BMW), in which the same sample is run by LC-MS in both liquid chromatography solvent with 14 NH 3 -acetate buffer, and in solvent with the buffer modified with 15 NH 3 -formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Altogether, it identified 26% of ~ 27,000 liver LC-MS features as putative metabolites, of which ~ 2600 showed HMDB or KEGG database formula match. This workflow is well-suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Here, in this paper, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. Here we report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of “unknown unknown” trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗