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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Localization and mass spectra of various matter fields on scalar-tensor brane

Recently, a new scalar-tensor braneworld model was presented in [http://dx.doi.org/10.1103/PhysRevD.86.127502]. It not only solves the gauge hierarchy problem but also reproduces a correct Friedmann-like equation on the brane. In this new model, there are two different brane solutions, for which the mass spectra of gravity on the brane are the same. In this paper, we investigate localization and mass spectra of various bulk matter fields (i.e., scalar, vector, Kalb-Ramond, and fermion fields) on the brane. It is shown that the zero modes of all the matter fields can be localized on the positive tension brane under some conditions, and the mass spectra of each kind of bulk matter field for the two brane solutions are different except for some special cases, which implies that the two brane solutions are not physically equivalent. When the coupling constants between the dilaton and bulk matter fields take special values, the mass spectra for both solutions are the same, and the scalar and vector zero modes are localized on the negative tension brane, while the KR zero mode is still localized on the positive tension brane.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Spectral probabilities of top-down tandem mass spectra

In mass spectrometry (MS)-based proteomics, accurate estimation of statistical signicance of peptide and protein identications is desired for determining whether they are actually correct. Probabilistic models, such as the generating function method, have been successfully applied to compute statistical signicance of peptide-spectrum matches (PSMs) in bottom-up MS, but it is limited to PSMs of short peptides without post-translational modications (PTMs). Recently, top-down MS has be- come available in many laboratories, which often identies intact proteins with PTMs. In this paper, we propose an extended generating function (EGF) method for accurately computing statistical signicance of protein- spectrum matches (PrSMs) with PTMs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

QC-GN 2 oMS 2 : a Graph Neural Net for High Resolution Mass Spectra Prediction

Predicting the mass spectrum of a molecular ion is often accomplished via three generalized approaches: rules-based methods for bond breaking, deep learning, or quantum chemical (QC) modeling. Rules-based approaches are often limited by the conditions for different chemical subspaces and perform poorly under chemical regimes with few defined rules. QC modeling is theoretically robust but requires significant amounts of computational time to produce a spectrum for a given target. Among deep learning techniques, graph neural networks (GNNs) have performed better than previous work with fingerprint-based neural networks in mass spectra prediction. To explore this technique further, we investigate the effects of including quantum chemically derived information as edge features in the GNN to increase predictive accuracy. The models we investigated include categorical bond order, bond force constants derived from extended tight-binding (xTB) quantum chemistry, and acyclic bond dissociation energies. Throughout this work, we evaluated these models against a control GNN with no edge features in the input graphs. Bond dissociation enthalpies yielded the best improvement with a cosine similarity score of 0.462 relative to the baseline model (0.437). In this work we also apply dynamic graph attention which improves performance on benchmark problems and supports the inclusion of edge features. Between implementations, we investigate the nature of the molecular embedding for spectra prediction and discuss the recognition of fragment topographies in distinct chemistries for further development in tandem mass spectrometry prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty “large” Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Multiplexed Post-Experimental Monoisotopic Mass Refinement ( m PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. The method, “multiplexed post-experiment monoisotopic mass refinement” (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/ MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, mPE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2011

Higher-Order Mass Defect Analysis for Mass Spectra of Complex Organic Mixtures

Higher-order mass defect analysis is introduced as a unique formula assignment and visualization method for the analysis of complex mass spectra. This approach is an extension of the concepts of Kendrick mass transformation widely used for identification of homologous compounds differing only by a number of base units (e.g., CH2, H2, O, CH2O, etc.) in complex mixtures. We present an iterative renormalization routine for defining higher order homologous series and multidimensional clustering of mass spectral features. This approach greatly simplifies visualization of complex mass spectra and increases the number of chemical formulae that can be confidently assigned for given mass accuracy. The potential for using higher-order mass defects for data reduction and visualization is shown. Higher-order mass defect analysis is described and demonstrated through third-order analysis of a de-isotoped high-resolution mass spectrum of crude oil containing nearly 13,000 peaks.

02 PETROLEUM↗
DOE OSTI2025

General search for supersymmetric particles in scenarios with compressed mass spectra using proton-proton collisions at $\sqrt{s}$ = 13 TeV

A general search is presented for supersymmetric particles (sparticles) in scenarios featuring compressed mass spectra using proton-proton collisions at a center-of-mass energy of 13 TeV, recorded with the CMS detector at the LHC. The analyzed data sample corresponds to an integrated luminosity of 138 fb −1 . A wide range of potential sparticle signatures are targeted, including pair production of electroweakinos, sleptons, and top squarks. The search focuses on events with a high transverse momentum system from initial-state-radiation jets recoiling against a potential sparticle system with significant missing transverse momentum. Events are categorized based on their lepton multiplicity, jet multiplicity, number of 𝑏-tagged jets, and kinematic variables sensitive to the sparticle masses and mass splittings. The sensitivity extends to higher parent sparticle masses than previously probed at the LHC for production of pairs of electroweakinos, sleptons, and top squarks with mass spectra featuring small mass splittings (compressed mass spectra). The observed results demonstrate agreement with the predictions of the background-only model. Lower mass limits are set at 95% confidence level on production of pairs of electroweakinos, sleptons, and top squarks that extend to 325, 275, and 780 GeV, respectively, for the most favorable compressed mass regime cases.

Hadron colliders↗
DOE OSTI2024

On the instrument-dependent appearance of ion dissociation events in atom probe tomography mass spectra

The successful application of atom probe tomography (APT) relies on the accurate interpretation of the mass spectrum (i.e. m/z histogram) from a sample. Some materials yield mass spectra that are amenable to a straightforward peak assignment/ranging, however, there are many materials that produce mass spectra with features that defy simple interpretation. One such example is Ga 2 O 3 which yields mass spectra containing several broad and difficult to interpret features. Herein, we study the GaO 2+ → O 1+ + Ga 1+ dissociation and we explain how this dissociation process gives rise to broad and previously unassigned features in the mass spectrum. Trajectory simulations are performed for the dissociation reaction utilizing realistic electrostatic models and compared to experiments using commercially available straight flight and reflectron based local electrode (LE) APT instruments. It is shown that the appearance of these features is strongly dependent on the specific design of the time-of-flight (ToF) mass analyzer. Additionally, we explore how various experimental parameters can affect the appearance of the dissociation process in the one-dimensional (1D) mass spectrum and in the two-dimensional (2D) correlation histogram. While the focus of this work is on a particular dissociation process related to Ga 2 O 3 , the understanding gained in the course of these simulations and experiments should be applicable to the interpretation of dissociation processes in other materials.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Anatomy of Protein Electrospray Ionization Mass Spectra by Superconducting Tunnel Junction Mass and Energy Spectrometry

Cryogenic superconducting tunnel junction (STJ) detectors have the advantage of single-particle sensitivity, high quantum efficiency, low noise, and the ability to detect the time and relative impact energy of deposited ions. This makes them attractive for use in mass spectrometry (MS) and as a form of energy spectrometry. STJ cryodetectors have been coupled to time-offlight (TOF) mass spectrometers equipped with a matrix-assisted laser desorption ionization (MALDI) source and to an electrospray ionization (ESI) TOF mass spectrometer. Here, a lab-made linear ion trap (LIT) mass spectrometer system was coupled to an ESI source and a 16-channel Nb-STJ array with improved readout electronics. The goal was to investigate fundamentals of ESI-generated protein ions by further exploiting the advantage of resolving these ions in a third dimension of the relative energy deposited into the STJs. The proteins equine cytochrome c, bovine carbonic anhydrase, bovine serum albumin, and murine immunoglobulin G were studied using this ESI-LIT-STJ-MS instrument. Multiply charged monomers, multimers, and fragments from metastable ions were resolved from monomer peaks by differences in ion deposition energy even when these ions have the same mass-to-charge ratio as the corresponding monomer. The determination of fragment mass from metastable decomposition is accomplished without knowing the charge state of the fragment. The average charge state of the multimers is reduced with each addition of a protein which is a direct reflection of the surface area available for charging. Multiply charged in-source fragments have also been observed and distinguished in the mass spectrum of carbonic anhydrase by using the differences in the energy deposited in the STJs.

42 ENGINEERING↗
DOE OSTI2023

A Machine Learning Model for Predicting Composition of Catalytic Coprocessing Products from Molecular Beam Mass Spectra

Demand for the development of an automated and integrated refining process for biofuels has increased in recent years due to the lack of generalized process inspection tools. In bio-oil upgrading processes, all process variables are maintained based on the offline specification of intermediates and products. A lack of real-time product specifications in batch-wise monitoring can cause process failure and wasted resources. Therefore, there is a need for a fast and accurate intermediates/product specification tool that can be used for real-time specification to reduce waste and mitigate the risk of process failure. Here, to address this gap, we developed a machine learning (ML) model for predicting speciated bio-oil composition, including paraffin, iso-paraffins, olefins, naphthene, and aromatics. The model is trained using the mass spectra from upgraded products collected in the vapor phase before condensation and predicts the composition of the condensed product. Training ML models using raw mass spectra is challenging due to numerous overlapped peaks originating from different parent compounds. With this in mind, we propose a protocol that (i) transforms raw mass spectra to chemistry-inspired predefined features and (ii) trains decision tree-based models using these features. Our results show that the random forest model was robust against overfitting and had the highest accuracy compared to other models. Moreover, a stochastic ablation method determined the eight most significant features while maximizing the accuracy. Our protocol facilitates real-time compositional analysis of upgraded bio-oils and thus real-time process monitoring. Additionally, this protocol enables the rational design of efficient catalysts and the determination of optimal process conditions.

09 BIOMASS FUELS↗
DOE OSTI2016

Applications and limitations of constrained high-resolution peak fitting on low resolving power mass spectra from the ToF-ACSM

The applicability, methods and limitations of constrained peak fitting on mass spectra of low mass resolving power ( m /Δ m 50 ~500) recorded with a time-of-flight aerosol chemical speciation monitor (ToF-ACSM) are explored. Calibration measurements as well as ambient data are used to exemplify the methods that should be applied to maximise data quality and assess confidence in peak-fitting results. Sensitivity analyses and basic peak fit metrics such as normalised ion separation are employed to demonstrate which peak-fitting analyses commonly performed in high-resolution aerosol mass spectrometry are appropriate to perform on spectra of this resolving power. Information on aerosol sulfate, nitrate, sodium chloride, methanesulfonic acid as well as semi-volatile metal species retrieved from these methods is evaluated. The constants in a commonly used formula for the estimation of the mass concentration of hydrocarbon-like organic aerosol may be refined based on peak-fitting results. Lastly, application of a recently published parameterisation for the estimation of carbon oxidation state to ToF-ACSM spectra is validated for a range of organic standards and its use demonstrated for ambient urban data.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Search for periodic signals in the dielectron and diphoton invariant mass spectra using 139 fb -1 of $pp$ collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

A search for physics beyond the Standard Model inducing periodic signals in the dielectron and diphoton invariant mass spectra is presented using 139 fb -1 of $\sqrt{s}$ = 13 TeV pp collision data collected by the ATLAS experiment at the LHC. Novel search techniques based on continuous wavelet transforms are used to infer the frequency of periodic signals from the invariant mass spectra and neural network classifiers are used to enhance the sensitivity to periodic resonances. In the absence of a signal, exclusion limits are placed at the 95% confidence level in the two-dimensional parameter space of the clock work gravity model. Model-independent searches for deviations from the background-only hypothesis are also performed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Primordial black holes and their mass spectra: The effects of mergers and accretion within stasis cosmologies

A variety of processes in the very early Universe can give rise to a population of primordial black holes (PBHs) with an extended mass spectrum. For certain mass spectra of this sort, it has been shown that the evaporation of these PBHs into radiation can drive the universe toward an epoch of cosmological stasis which can persist for a significant number of 𝑒-folds of cosmological expansion. However, in general, the initial mass spectrum which characterizes a population of PBHs at the time of production can subsequently be distorted by processes such as mergers and accretion. Here, in this paper, we examine the effects that these processes have on the spectra that lead to a PBH-induced stasis. Within such stasis models, we find that mergers have only a negligible effect on these spectra within the regime of interest for stasis. We likewise find that the effect of accretion is negligible in many cases of interest. However, we find that the effect of accretion on the PBH mass spectrum is non-negligible in situations in which this spectrum is particularly broad. In such situations, the stasis epoch is abridged or, in extreme cases, does not occur at all. Thus accretion plays a nontrivial role in constraining the emergence of stasis within scenarios which lead to extended PBH mass spectra.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Search for physics beyond the standard model in dilepton mass spectra in proton-proton collisions at √s = 8 TeV

Dimuon and dielectron mass spectra, obtained from data resulting from proton-proton collisions at 8 TeV and recorded by the CMS experiment, are used to search for both narrow resonances and broad deviations from standard model predictions. The data correspond to an integrated luminosity of 20.6 (19.7) fb –1 for the dimuon (dielectron) channel. No evidence for non-standard-model physics is observed and 95% confidence level limits are set on parameters from a number of new physics models. The narrow resonance analyses exclude a Sequential Standard Model Z SSM ' resonance lighter than 2.90 TeV, a superstring-inspired Z ψ ' lighter than 2.57 TeV, and Randall-Sundrum Kaluza-Klein gravitons with masses below 2.73, 2.35, and 1.27 TeV for couplings of 0.10, 0.05, and 0.01, respectively. A notable feature is that the limits have been calculated in a model-independent way to enable straightforward reinterpretation in any model predicting a resonance structure. The observed events are also interpreted within the framework of two non-resonant analyses: one based on a large extra dimensions model and one based on a quark and lepton compositeness model with a left-left isoscalar contact interaction. Lower limits are established on MS, the scale characterizing the onset of quantum gravity, which range from 4.9 to 3.3 TeV, where the number of additional spatial dimensions varies from 3 to 7. Thus lower limits on Λ, the energy scale parameter for the contact interaction, are found to be 12.0 (15.2) TeV for destructive (constructive) interference in the dimuon channel and 13.5 (18.3) TeV in the dielectron channel.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.

data analysis↗