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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 OSTI2017

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

Successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development of pregnancy related problems at the molecular level. In this perspective, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2024

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

An analysis of nuclear fuel burnup in the AGR-1 TRISO fuel experiment using gamma spectrometry, mass spectrometry, and computational simulation techniques

AGR 1 was the first in a series of experiments designed to test US TRISO fuel under high temperature gas-cooled reactor irradiation conditions. This experiment was irradiated in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) and is currently undergoing post irradiation examination (PIE) at INL and Oak Ridge National Laboratory. One component of the AGR 1 PIE is the experimental evaluation of the burnup of the fuel by two separate techniques. Gamma spectrometry was used to non destructively evaluate the burnup of all 72 of the TRISO fuel compacts that comprised the AGR 1 experiment. Two methods for evaluating burnup by gamma spectrometry were developed, one based on the Cs 137 activity and the other based on the ratio of Cs 134 and Cs 137 activities. Burnup values determined from both methods compared well with the values predicted from simulations. The highest measured burnup was 20.1% FIMA for the direct method and 20.0% FIMA for the ratio method (compared to 19.56% FIMA from simulations). An advantage of the ratio method is that the burnup of the cylindrical fuel compacts can determined in small (2.5 mm) axial increments and an axial burnup profile can be produced. Destructive chemical analysis by inductively coupled mass spectrometry (ICP MS) was then performed on selected compacts that were representative of the expected range of fuel burnups in the experiment to compare with the burnup values determined by gamma spectrometry. The compacts analyzed by mass spectrometry had a burnup range of 19.3% FIMA to 10.7% FIMA. The mass spectrometry evaluation of burnup for the four compacts agreed well with the gamma spectrometry burnup evaluations and the expected burnup from simulation. For all four compacts analyzed by mass spectrometry, the maximum range in the three experimentally determined values and the predicted value was 6% or less. Furthermore, the results confirm the accuracy of the nondestructive burnup evaluation from gamma spectrometry for TRISO fuel compacts across a burnup range of approximately 10 to 20% FIMA and also validate the approach used in the physics simulation of the AGR 1 experiment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Ion mobility spectrometry–mass spectrometry (IMS–MS) for on- and offline analysis of atmospheric gas and aerosol species

Abstract. Measurement techniques that provide molecular-level information are needed to elucidate the multiphase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS–MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS–MS after ionization with a custom-built nitrate chemical ionization (CI) source. This CI–IMS–MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS) ambient field campaign in the forested SE US. The ambient IMS–MS signals are consistent with laboratory IMS–MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-D IMS–MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS–MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. Controlled fragmentation of precursor ions by collisionally induced dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.

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

Atmospheric Solid Analysis Probe Coupled to Ion Mobility Spectrometry-Mass Spectrometry, a Fast and Simple Method for Polyalphaolefin Characterization

Polyalphaolefins (PAOs) are polymers produced from linear alpha olefins through catalytic oligomerization processes. The PAOs are known as synthetic high-performance base stock fluids used to improve the efficiency of many other synthetic products. In this study, we report the direct characterization of PAOs using atmospheric solid analysis probe (ASAP) coupled with ion mobility spectrometry-mass spectrometry (IMS-MS). We studied different PAOs grades exhibiting low- and high-viscosity index. Specific adjustments of the ASAP source parameters permitted the monitoring of ionization processes as three mechanisms could occur for these compounds: hydride abstraction, nitrogen addition, and/or the formation of [M−2H]{sup +•} ions. Several series of fragment ions were obtained, which allowed the identification of the alpha olefin used to synthesize the PAO. The use of the ion mobility separation dimension provides information on isomeric species. In addition, the drift time versus m/z plots permitted rapid comparison between PAO samples and to evidence their complexity. These 2D plots appear as fingerprints of PAO samples. To conclude, the resort to ASAP-IMS-MS provides a rapid characterization of the PAO samples in a direct analysis approach, without any sample preparation. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate (in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

mzapy : An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format

We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of a core library with standard mass spectrometry utilities greatly facilitates fast software development. Here, we present a Python library, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python with minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multi-omics domain. The free and open source mzapy is built with extensibility in mind, and future development will support cloud computing and artificial intelligence/machine learning applications. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.

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

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules such as proteins and lipids, and alter their properties and functions, so understanding the effect glycans have on cellular systems is essential. However the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycan standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

Structural Elucidation of cis / trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2021

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry

Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry–Mass Spectrometry

The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a “bead-on-a-string” appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry–Mass Spectrometry

Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. In conclusion, we first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Differential Mobility Spectrometry-Mass Spectrometry (DMS-MS) in Radiation Biodosimetry: Rapid and High-Throughput Quantitation of Multiple Radiation Biomarkers in Nonhuman Primate Urine

High-throughput methods to assess radiation exposure are a priority due to concerns that include nuclear power accidents, the spread of nuclear weapon capability, and the risk of terrorist attacks. Metabolomics, the assessment of small molecules in an easily accessible sample, is the most recent method to be applied for the identification of biomarkers of the biological radiation response with a useful dose-response profile. Profiling for biomarker identification is frequently done using an LC-MS platform which has limited throughput due to the time-consuming nature of chromatography. We present here a chromatography-free simplified method for quantitative analysis of seven metabolites in urine with radiation dose-response using urine samples provided from the Pannkuk et al. (2015) study of long-term (7-day) radiation response in nonhuman primates (NHP). The stable isotope dilution (SID) analytical method consists of sample preparation by strong cation exchange-solid phase extraction (SCX-SPE) to remove interferences and concentrate the metabolites of interest, followed by differential mobility spectrometry (DMS) ion filtration to select the ion of interest and reduce chemical background, followed by mass spectrometry (overall SID-SPE-DMS-MS). Since no chromatography is used, calibration curves were prepared rapidly, in under 2 h (including SPE) for six simultaneously analyzed radiation biomarkers. The seventh, creatinine, was measured separately after 2500× dilution. Creatinine plays a dual role, measuring kidney glomerular filtration rate (GFR), and indicating kidney damage at high doses. The current quantitative method using SID-SPE-DMS-MS provides throughput which is 7.5 to 30 times higher than that of LC-MS and provides a path to pre-clinical radiation dose estimation. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Performance Enhancements in Differential Ion Mobility Spectrometry-Mass Spectrometry (DMS-MS) by Using a Modified CaptiveSpray Source

Differential ion mobility spectrometry (DMS) spatially separates ions in the gas phase using the mobility differences of the ions under applied low and high electric fields. The use of DMS as an ion filter (or ion selector) prior to mass spectrometry analysis has been compromised by the limited ion transmission efficiency. This paper reports enhancement of the DMS-MS sensitivity and signal stability using a modified CaptiveSpray™ source. In terms of the ion sampling and transmission efficiency, the modified CaptiveSpray source swept ~ 89% of the ions generated by the tapered capillary through the DMS device (compared to ~ 10% with a conventional microspray source). The signal fluctuation improved from 11.7% (relative standard deviation, RSD) with microspray DMS-MS to 3.6% using CaptiveSpray-DMS-MS. Coupling of LC to DMS-MS via the modified CaptiveSpray source was simple and robust. Using DMS as a noise-filtering device, LC-DMS-MS performed better than conventional LC-MS for analyzing a BSA digest standard. Although LC-DMS-MS had a lower sequence coverage (55%), a higher Mascot score (283) was obtained compared to those of LC-MS (sequence coverage 65%; Mascot score 192) under the same elution conditions. The improvement in the confidence of the search result was attributed to the preferential elimination of noise ions. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry–Mass Spectrometry Lipidomics Data

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ion Mobility Spectrometry-Mass Spectrometry for High-Throughput Analysis

Ion mobility spectrometry is a widely used analytical technique providing gas phase separation of molecules. It has received increasing attention in the recent years with the advancement in technology development and the availability of commercial instruments. In this chapter, we introduced the ion mobility fundamental theory and provided examples of IMS applications, especially for isomer separation, collision cross section database generation, high throughput analysis workflows, software tools for IMS data analysis, and ongoing high resolution SLIM IMS development. While IMS is not yet routinely utilized in drug discovery and pharmaceutical industry, there has been increased interest in high throughput library screening and antibody characterization. With all the ongoing development in IMS technology and informatics, we foresee more and more exciting applications of high throughput IMS analysis in different fields including omics studies, drug discovery and clinical applications in the near future.

Ross, Dylan H.↗
DOE OSTI2018

Utilizing ion mobility spectrometry and mass spectrometry for the analysis of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polybrominated diphenyl ethers and their metabolites

Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are persistent environmental pollutants originating from incomplete combustion of organic materials and synthetic sources. PAHs, PCBs, and PBDEs have all been shown to have a significant effect on human health with correlations to cancer and other diseases. Therefore, measuring the presence of these xenobiotics in the environment and human body is imperative for assessing their health risks. To date, their analyses require both gas chromatography and liquid chromatography separations in conjunction with mass spectrometry measurements for detection of both the parent molecules and their hydroxylated metabolites, making their studies extremely time consuming. In this work, we characterized PAHs, PCBs, PBDEs and their hydroxylated metabolites using ion mobility spectrometry coupled with mass spectrometry (IMS-MS) and in combination with different ionization methods including electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). The collision cross section and m/z trend lines derived from the IMS-MS analyses displayed distinct trends for each molecule type. Additionally, the rapid isomeric and molecular separations possible with IMS-MS showed great promise for quickly distinguishing the parent and metabolized PAH, PCB, and PDBE molecules in complex environmental and biological samples.

Zheng, Xueyun (ORCID:0000000197824521)↗