Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MASS SPECTRA”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

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↗
NASA NTRS1991

Interpretation of the ion mass spectra in the mass per charge range 25-35 amu/e obtained in the inner coma of Halley's comet by the HIS-sensor of the Giotto IMS experiment

The IMS-HIS double-focusing mass spectrometer that flew on the Giotto spacecraft covered the mass per charge range from 12 to 56 (amu/e). By comparing flight data, calibration data and results of model calculations of the ion population in the inner coma, the absolute mass scale is established, and ions in the mass range 25 to 35 are identified. Ions resulting from protonation of molecules with high proton affinity are relatively abundant, enabling us to estimate relative source strengths for H2CO, CH3OH, HCN, and H2S, providing for the first time a positive in situ measurement of methanol. Also, upper limits for NO and some hydrocarbons are derived.

Geiss, J.↗
NASA NTRS1991

Interpretation of the ion mass spectra in the mass range 25-35 obtained in the inner coma of Halley's comet by the HIS-sensor of the Giotto IMS Experiment

The IMS-HIS double-focussing mass spectrometer that flew on the Giotto spacecraft covered the mass per charge range from 12 to 56 (AMU/e). By comparing flight data, calibration data, and results of model calculations of the ion population in the inner coma, the absolute mass scale is established, and ions in the mass range 25 to 35 are identified. Ions resulting from protonation of molecules with high proton affinity are relatively abundant, enabling us to estimate relative source strengths for H2CO, CH3OH, HCN, and H2S, providing for the first time a positive in situ measurement of methanol. Also, upper limits for NO and some hydrocarbons are derived.

Geiss, J.↗
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↗
NASA NTRS2019

Decomposition of Electron Ionization Mass Spectra for Space Application Using a Monte-Carlo approach

Rationale: Quadrupole mass spectrometers equipped with an electron ionization (EI) sources have been widely used in space exploration to investigate the composition of planetary surfaces and atmospheres. However, the complexity of the samples and the minimal calibration for the fragmentation of molecules in the ionization chambers have prevented the deconvolution of the majority of the mass spectra obtained at different targets, thus limiting the determination of the exact composition of the samples analyzed. We propose a Monte‐Carlo approach to solve this issue mathematically. Methods: We decomposed simulated mass spectra of mixtures acquired with unit resolving power mass spectrometers and EI sources into the sum of the single components fragmentation patterns weighted by their relative concentration using interior‐point least‐square fitting. To fit compounds with poorly known fragmentation patterns, we used a Monte‐Carlo method to vary the intensity of individual fragment ions. We then decomposed the spectrum thousands of times to obtain a statistical distribution. Results: By performing the deconvolution on a mixture of seven different molecules with interfering fragmentation patterns (H2O, O2, CH4, Ar, N2, C2H4, and C2H6) we show that this approach retrieves the mixing ratio of the individual components more accurately than regular mass spectra decomposition methods that rely on fragmentation patterns from general databases. It also provides the probability density function for each species's mixing ratio. Conclusions: By removing the solution degeneracy in the decomposition of mass spectra, the method described herein could significantly increase the scientific retrieval from archived space flight mass spectrometry data, where calibration of the ionization source is no longer an option.

Thomas Gautier↗
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↗
NASA NTRS1991

Preliminary results of investigations into the use of artificial neural networks for discriminating gas chromatograph mass spectra of remote samples

Neural networks trained using mass spectra data from the National Institute of Standards and Technology (NIST) are studied. The investigations also included sample data from the gas chromatograph mass spectrometer (GCMS) instrument aboard the Viking Lander, obtained from the National Space Science Data Center. The work performed to data and the preliminary results from the training and testing of neural networks are described. These preliminary results are presented for the purpose of determining the viability of applying artificial neural networks in discriminating mass spectra samples from remote instrumentation such as the Mars Rover Sample Return Mission and the Cassini Probe.

Geller, Harold A.↗
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↗
NASA NTRS1988

PIA update: Correlation analyses of mass spectra

The PIA instrument aboard the Giotto spacecraft (a time of flight spectrometer) has been presented elsewhere. The mass spectra used in this analysis were decoded and mass numbers assigned according to the presence of carbon and silver, using the global values for these elements in their spectral absence. The results presented here were obtained using a frequency of occurrence based on analysis which correlated how often mass numbers appear in the mass spectra and which mass numbers tend to occur together in the same spectra; no amplitude information is utilized. The data are presented as plots of mass vs coincident mass for different subsets of the PIA data set, with both axes having units of atomic mass. Frequency contours are plotted at approximately five percent contour intervals, relative to the maximum AMU occurrence in that plot. The plots presented are symmetrical about the matrix diagonal, i.e., every mass is coincident with itself in a given spectra.

Mason, L. W.↗
NASA NTRS2017

Mass Spectra Deconvolution of Gaseous Mixtures Containing Volatile Organic Compounds

The Spacecraft Atmosphere Monitor (S.A.M.) analyzes all gaseous pollutants in the 1-150Th mass-to-charge range based on their positive-ion mass spectra. Of particular interest is the Trace Gas Analysis (TGA) mode of operation in which S.A.M detects minute amounts of volatile organic compounds (VOC). Pollutant component of the ambient air is sampled on demand in twenty full mass spectra per second. All spectra is accumulated in two-second intervals by an on-board Field Programmable Gate Arrays (FPGA) unit. Mass spectra represents the number of detected fragment ions in a given mass-to-charge ratio channel. Electron impact ionization of neutral molecules results in creation of numerous fragment ions and most of organic compounds will contribute several identical fragments. Despite the presence of these molecular isobars, we developed the deconvolution algorithm capable of identifying target species based on their characteristic fragmentation patterns. We investigate the efficiency of deconvolution algorithm as a function of mass resolution with which mass spectrum is acquired. Higher the mass resolution, better the chances are to distinguish between stereoisomers using their fragmentation propensities, but also results in higher data volumes to be processed by a set of small footprint software stacks hosted by an on-board computer. Finding the balance between deconvolution accuracy and generated data volume under time constrains and limited computing resources is the main topic of this study.

Darrach, M.↗
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↗