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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 OSTI2018

An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can easily cause problems if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases with highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.

Environmental Molecular Sciences Laboratory↗
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 OSTI2017

Distinguishing d - and l -aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry

Ion mobility spectrometry (IMS) was utilized to separate Aβ peptide variants containing isomeric asparic and isoaspartic acid residues with either a l - or d -form. The abundance of each variant is of great interest in Alzheimer's disease studies and also to evaluate how often these modifications are occurring in other environmental and biological samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Monolithic collimator and energy analyzer for ion spectrometry

Disclosed are various examples related to ion or particle spectrometry utilizing a monolithic collimator and energy analyzer. In one example, a particle selection device includes a single substrate including a curved channel energy analyzer section and a straight channel collimator section, wherein particles pass through the collimator section and enter the energy analyzer section of the substrate. The channel outlets in the collimator section are aligned with the channel inlets of the energy analyzer section. Electric and/or magnetic fields can be applied across the channels of the energy analyzer for ion or particle discrimination. A particle detector at the outlet of the energy analyzer section can provide indications of detected ions and/or particles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Native Mass Spectrometry, Ion mobility, and Collision-Induced Unfolding Categorize Malaria Antigen/Antibody Binding

Plasmodium vivax Duffy Binding Protein (PvDBP) is a promising vaccine candidate for P. vivax malaria. Recently, we reported the epitopes on PvDBP region II (PvDBP-II) for three inhibitory monoclonal antibodies (2D10, 2H2, and 2C6). In this communication, we describe the combination of native mass spectrometry and ion mobility (IM) with collision induced unfolding (CIU) to study the conformation and stabilities of three malarial antigen–antibody complexes. These complexes, when collisionally activated, undergo conformational changes that depend on the location of the epitope. CIU patterns for PvDBP-II in complex with antibody 2D10 and 2H2 are highly similar, indicating comparable binding topology and stability. A different CIU fingerprint is observed for PvDBP-II/2C6, indicating that 2C6 binds to PvDBP-II on an epitope different from 2D10 and 2H2. This work supports the use of CIU as a means of classifying antigen-antibody complexes by their epitope maps in a high throughput screening workflow. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Native Mass Spectrometry, Ion Mobility, Electron-Capture Dissociation, and Modeling Provide Structural Information for Gas-Phase Apolipoprotein E Oligomers

Apolipoprotein E (apoE) is an essential protein in lipid and cholesterol metabolism. Although the three common isoforms in humans differ only at two sites, their consequences in Alzheimer’s disease (AD) are dramatically different: only the ε4 allele is a major genetic risk factor for late-onset Alzheimer’s disease. The isoforms exist as a mixture of oligomers, primarily tetramer, at low μM concentrations in a lipid-free environment. This self-association is involved in equilibrium with the lipid-free state, and the oligomerization interface overlaps with the lipid-binding region. Elucidation of apoE wild-type (WT) structures at an oligomeric state, however, has not yet been achieved. To address this need, we used native electrospray ionization and mass spectrometry (native MS) coupled with ion mobility (IM) to examine the monomer and tetramer of the three WT isoforms. Although collision-induced unfolding (CIU) cannot distinguish the WT isoforms, the monomeric mutant (MM) of apoE3 shows higher stability when submitted to CIU than the WT monomer. From ion-mobility measurements, we obtained the collision cross section and built a coarse-grained model for the tetramer. Application of electron-capture dissociation (ECD) to the tetramer causes unfolding starting from the C-terminal domain, in good agreement with solution denaturation data, and provides additional support for the C4 symmetry structure of the tetramer. .

62 RADIOLOGY AND NUCLEAR MEDICINE↗
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 OSTI2018

Stimulated Motion Suppression (STMS): a New Approach to Break the Resolution Barrier for Ion Trap Mass Spectrometry

Ion trap is an excellent platform to perform tandem mass spectrometry (MS/MS), but has an intrinsic drawback in resolving power. Using ion resonant ejection as an example, the resolution degradation can be largely attributed to the broadening of the resonant frequency band (RFB) between ion motion and driving alternative-current (AC). To solve this problem, stimulated motion suppression (STMS) was developed. The key idea of STMS is the use of two suppression alternative-current (SAC) signals, which both have reversed initial phases to the main AC. The SACs can block the unexpected sideband ion resonances (or ejections), therefore playing a key role in sharpening the RFB. The proof-of-concept has been demonstrated through ion trajectory simulations and validated experimentally. STMS provides a new and versatile means for the improvement of the ion trap resolution, which for a long time has reached the bottleneck through conventional methods, e.g., increasing the radio-frequency (RF) voltage and decreasing the mass scan rate. At the end, it is worth noting that the idea of STMS is very general and principally can be applied in any RF device for the purposes of high-resolution mass analysis and ion isolation. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Evaluation of micromilling/conventional isotope ratio mass spectrometry and secondary ion mass spectrometry of δ 18 O values in fish otoliths for sclerochronology

Stable oxygen isotope ratios (δ 18 O values) measured in fish otoliths can provide valuable detailed information on fish life history, fish age determination, and ocean thermography. Traditionally, otoliths are sampled by micromilling followed by isotope ratio mass spectrometry (IRMS), but direct analysis by secondary ion mass spectrometry (SIMS) is becoming more common. However, these two methods have not been compared to determine which, if either, is better for fish age validation studies. Hence, the goals were to: (1) determine if the δ 18 O signatures from the two different methods are similar, (2) determine which method is better for fish age validation studies, and (3) examine biogeographic and migration history. Both analytical techniques, micromilling/IRMS and SIMS, were used to measure δ 18 O values in six Pacific cod (Gadus macrocephalus) otoliths. A series of measurements was made from the center of each otolith to its edge to develop a life-history δ 18 O signature for each fish. The sampling resolution of SIMS analyses was 2–3 times greater than that obtained by micromilling/IRMS. We found an offset between SIMS and micromilling/IRMS δ 18 O values, about 0.5‰ on average, with SIMS yielding lower values. However, the δ 18 O patterns from both methods (i.e., the number of δ 18 O maxima) correspond to the estimated age determined by otolith growth-zone counts, validating fish age determination methods. Both techniques resolved δ 18 O life-history signatures and showed patterns consistent with seasonal variation in temperatures and changes due to fish migration. When otoliths are large, micromilling/IRMS can provide adequate resolution for fish age validation. Finally, SIMS is the better option if greater sampling resolution is required, such as when otoliths are small or specimens are longer lived and have compact growth zones.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Ion Mobility Spectrometry with High Ion Utilization Efficiency Using Traveling Wave-Based Structures for Lossless Ion Manipulations

Ion packets introduced from gates, ion funnel traps, and other conventional ion injection mechanisms produce ion pulse widths typically around a few microseconds or less for ion mobility spectrometry (IMS)-based separations on the order of 100 milliseconds. When such ion injection techniques are coupled with ultralong path length traveling wave (TW)-based IMS separations (i.e., on the order of seconds) using structures for lossless ion manipulations (SLIMs), typically very low ion utilization efficiency is achieved for continuous ion sources [e.g., electrospray ionization (ESI)]. Even with the ability to trap and accumulate much larger populations of ions than being conventionally feasible over longer time periods in SLIM devices, the subsequent long separations lead to overall low ion utilization. In this study, we report the use of a highly flexible SLIM arrangement, enabling concurrent ion accumulation and separation and achieving near-complete ion utilization with ESI. We characterize the ion accumulation process in SLIM, demonstrate >98% ion utilization, and show both increased signal intensities and measurement throughput. This approach is envisioned to have broad utility to applications, for example, involving the fast detection of trace chemical species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Effective Ion Mobility Peak Width as a New Isomeric Descriptor for the Untargeted Analysis of Complex Mixtures Using Ion Mobility-Mass Spectrometry

Ion mobility coupled with mass spectrometry was proven to be an efficient way to characterize complex mixtures such as petroleum samples. However, the identification of isomeric species is difficult owing to the molecular complexity of petroleum and no availability of standard molecules. This paper proposes a new simple indicator to estimate the isomeric content of highly complex mixtures. This indicator is based on the full width at half maximum (FWHM) of the extracted ion mobility peak measured in millisecond or square angstrom that is corrected for instrumental factors such as ion diffusion. This value can be easily obtained without precisely identifying the number of isomeric species under the ion mobility peaks. Considering the Boduszynski model, the ion mobility profile for a particular elemental composition is expected to be a continuum of various isomeric species. The drift time-dependent fragmentation profile was studied and confirmed this hypothesis, a continuous evolution of the fragmentation profile showing that the larger alkyl chain species were detected at higher drift time values. This new indicator was proven to be a fast and efficient method to compare vacuum gas oils for which no difference was found using other analytical techniques. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Concomitant ion effects on isotope ratio measurements with liquid sampling – atmospheric pressure glow discharge ion source Orbitrap mass spectrometry

RATIONALE: The field of highly accurate and precise isotope ratio (IR) analysis has been dominated by inductively coupled plasma and thermal ionization mass spectrometers. While these instruments are considered the gold standard for IR analysis, the International Atomic Energy Agency desires a field deployable instrument capable of accurately and precisely measuring U isotope ratios. METHODS: The proposed system interfaces the liquid sampling – atmospheric pressure glow discharge (LS-APGD) ion source with a high resolution Exactive Orbitrap mass spectrometer. With this experimental setup certified U isotope standards and unknown samples were analyzed. The accuracy and precision of the system were then determined. RESULTS: The LS-APGD /Exactive instrument measures a certified reference material of natural U (235U/238U = 0.007258) as 0.007041 with a relative standard deviation of 0.158% meeting the International Target Values for Uncertainty for the destructive analysis of U. Additionally, when three unknowns measured and compared to the results from an ICP multi collector instrument, there is no statistical difference between the two instruments. CONCLUSIONS: The LS-APGD / Orbitrap system, while still in the preliminary stages of development, offers highly accurate and precise IR analysis that suggest a paradigm shift in the world of IR analysis. Furthermore, the portability of the LS-APGD as an elemental ion source combined with the low overhead and small size of the Orbitrap suggest that the instrumentation is capable of being field deployable. With liquid sampling glow discharge-Orbitrap MS, isotope ratio and precision performance improves with rejection of concomitant ion species.

atmospheric pressure sampling↗
DOE OSTI2014

Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry with Time-of-Flight Mass Spectrometry

We report on the performance of Structures for Lossless Ion Manipulation (SLIM) devices as a means for transmitting ions and performing ion mobility separations (IMS). Ions were successfully transferred from an electrospray ionization (ESI) source to the TOF MS analyzer by means of a linear SLIM device and an alternative arrangement including a 90° turn. First, the linear geometry was optimized for radial confinement by tuning RF on the central ‘rung’ electrodes and potentials on the DC-only guard electrodes. Selecting an appropriate DC guard bias (2-6 V) and RF amplitude (≥160 Vp-p at 750 kHz) resulted in the greatest ion intensities. Close to ideal IMS resolving power was maintained over a range of applied voltages. Second, the 90° turn was optimized for radial confinement by tuning the RF on the rung electrodes and DC on the guard electrodes; however, both resolving power and ion transmission showed a dependence on these voltages and the best conditions for both were > 300 Vp-p RF (685 kHz) and 7-11 V guard DC bias. Both geometries provide IMS resolving powers at the theoretical limit (R~58), showing that the negative “racetrack” effect from turning around a corner can be successfully avoided, as well as the capability for essentially lossless ion transmission.

conveyor↗
DOE OSTI2018

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline’s ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗