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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Discovery of unknown posttranslational modifications by top-down mass spectrometry

Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.

Wilson, Jesse W.↗
DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

Iron-Isotopic Fractionation Studies Using Multiple Collector Inductively Coupled Plasma Mass Spectrometry

The importance of Fe biogeochemistry has stimulated interest in Fe isotope fractionation. Recent studies using thermal ionization mass spectrometry (TIMS) and a "double spike" demonstrate the existence of biogenic Fe isotope effects. Here, we assess the utility of multiple-collector inductively-coupled plasma mass spectrometry(MC-ICP-MS) with a desolvating sample introduction system for Fe isotope studies, and present data on Fe biominerals produced by a thermophilic bacterium. Additional information is contained in the original extended abstract.

Anbar, A. D.↗
DOE OSTI2022

Review of the Third Conference of the Imaging Mass Spectrometry Society (IMSS 3): Accounts of a Hybrid Virtual and In-Person Meeting and the State and Future of the Field

The third annual conference of the Imaging Mass Spectrometry Society (IMSS3) was held October 3–6, 2021 in a hybrid format that included virtual and in-person attendance (Colorado Springs, CO). In this work, we highlight many of the methods and applications presented, the state of the field, and some insights into the emerging areas in the field of imaging mass spectrometry. We also reflect upon the processes behind planning a hybrid conference and discuss the successes and challenges of the event in retrospect.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter across Laboratories

Non-targeted liquid chromatography tandem highresolution mass spectrometry (LC−MS/MS) is increasingly applied for the structure-resolved chemical analysis of dissolved organic matter (DOM). With new developments in MS instrumentation and analysis software, the approach has gained substantial momentum over the past decade. However, achieving high-quality analytical data that is reproducible and comparable across laboratories can be a bottleneck in non-targeted metabolomics and organic matter chemical analysis, especially for data reuse in repository-scale analyses. Understanding the capabilities as well as challenges of comparing LC−MS/MS data from different laboratories is necessary for inferring global trends from public data sets. To illuminate instrumentation factors that drive differences and variability, we used a standardized data analysis pipeline, including classical (CMN) and featurebased molecular networking (FBMN), to analyze data from a ring trial by 24 laboratories on identical sample sets of algal and DOM extracts that were mixed in predefined concentrations and spiked with standards. Our results showed that data sets from similar mass spectrometer types with unified instrument parameters were qualitatively comparable, resolving the same general trends and shared mass spectral features. Interlaboratory comparability was best for high-intensity features, while low-intensity features showed greater detection variability. Our analysis also highlights challenges when comparing data from instruments with different acquisition rates or operating with less standardized methods. Lastly, we provide recommendations for data integration, public data sharing, standardization, and best practices for standardized LC−MS/MS data acquisition, which will be critical for long-term time series and intercomparability of DOM chemical analyses.

DOM↗
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

133Xe Noble Gas Mass Spectrometry Measurement for High Purity Germanium Detector Performance Verification

Idaho National Laboratory produces quality control standards for laboratories that operate xenon radionuclide monitoring systems. Activities reported with each quality control standard are quantified using high purity germanium detectors. A collection of measurement capabilities are being set up at Idaho National Laboratory to establish an in-house high purity germanium detector performance verification system, with noble gas mass spectrometry being one of these measurement capabilities. The first noble gas mass spectrometry and high purity germanium measurement comparison is presented here. A Xe-133 gas sample was prepared and the activity was quantified with high purity germanium detectors. The Xe-133 sample was diluted with a known quantity of isotopically enriched Xe-126 gas; the resulting Xe-133 : Xe-126 atom ratio was calculated to be 1.15x10-4 +/- 2% at reference time t. An aliquot of this gas sample containing approximately 10 million Xe-133 atoms was introduced into a ThermoFisher Scientific Helix MC Plus noble gas mass spectrometer for analysis. The measured Xe-133 : Xe-126 atom ratio was determined to be 1.10x10-4 +/- 2% (1-sigma uncertainty) at reference time t, about 4.3% lower than the atom ratio determined with the measured high purity germanium activity.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
DOE OSTI2022

Uncertainty evaluation in reference material characterization by double isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS)

Double isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) is one of the most important measurement methods in the establishment of measurement standards for inorganic analysis. However, there is still no good consensus on approaches for uncertainty evaluation in double ID-ICP-MS. Particularly, approaches to treating the instrumental isotopic fractionation (IIF) phenomenon and correlation between uncertainty sources are diverse and often unclear in the literature. Here, an approach for uncertainty evaluation in double ID-ICP-MS measurements is described. Using three certified reference materials (CRMs), it is shown that the IIF effects cancel out and should not be included in the uncertainty budget. Further, a consistent way of considering correlated sources of uncertainty to prevent double counting of uncertainties is described in detail along with an example of measuring the mass fraction of magnesium in an oyster powder CRM.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

NWAL Validation Report for U Assay by Potentiometric Titration (Modified Davies and Gray Technique) and U and PU Assay by Isotope Dilution Mass Spectrometry

SRNL Sensing & Metrology, previously Analytical Laboratory, is a member of the IAEA Network of Analytical Laboratories for Nuclear Material Measurement that is qualified to provide Uranium and Plutonium isotopic analysis of nuclear materials by Thermal Ionization Mass Spectrometry. As part of the membership, SRNL participated in the 2019 Nuclear Material Round Robin to maintain the qualification to provide isotopic analysis. SRNL also participated with the additional intent to qualify Uranium Assay by Potentiometric Titration (Davies and Gray method) and Uranium and Plutonium Isotope Dilution by Thermal Ionization Mass Spectrometry as part of the International Atomic Energy Agency’s Network of Analytical Laboratories. The proficiency test exercise was conducted by the Office of Safeguards Analytical Services, Department of Safeguards.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements

Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, in this work, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Using Separation-Enhanced Isotope Ratio Mass Spectrometry to Enable Increased Renewable Carbon Content in Transportation Fuels (CRADA 525)

Stable isotope ratio measurements of carbon atoms using isotope ratio mass spectrometry (IRMS) can be an effective tool for quantifying biogenic carbon in co-processed fuels, with results approaching the precision and accuracy of accelerator mass spectrometry (AMS). The lower cost of an IRMS may enable deployment to refineries, improving access and analysis turnaround times (≤2 hours), and, by extension, provide data that can allow process optimization to maximize renewable carbon in desired refinery products. This project explored the integration of chemical separation with IRMS analyses to enable highly detailed tracking of biogenic carbon into fuel product streams separated by boiling point range, chemical class, or specific compound. Forty-nine fuels and fuel components of fossil and biogenic origin, spanning gasoline and diesel boiling point ranges, were received from three refiners and were analyzed for their δ 13 C values via IRMS. Results spanned a 13 C range from ca. 10‰ to 44‰ and reflect materials derived from sustainable sources (e.g., C4 or C3 plants, animal-based pathways, syngas) or from fossil-derived fuels. Common ranges are approximately 18‰ to 9‰ and approximately 30‰ to 20‰ for C4 and C3 plants, respectively, and approximately 34‰ to 24‰ and approximately 70‰ to 33‰ for petroleum-derived fuels and methane, respectively. Fuel-like standards were developed and tested using direct-injection elemental analyzer (EA) IRMS for liquid fuels. This method was compared with the published methods, yielding statistically similar results. Four blend curve sets were produced ranging from 0% to 100% of a fuel containing biogenic carbon, focusing on 0% to 10% biogenic carbon. Linear fits were the most applicable for two of the four blend curve sets; however, two sets were found to exhibit slightly quadratic behavior, which was more pronounced in low biogenic blend samples, necessitating second-order fits. The origin of the slight quadratic behavior remains unclear; however, the discussion points to possible interpretations. CanmetENERGY thoroughly characterized a majority of the samples using one- and two-dimensional gas chromatography (GC and GC×GC, respectively) and other analyses. Selected samples were subjected to solid phase extraction (SPE) for saturate, olefin, aromatic, and polar (SOAP) analysis, and the resulting solvent-diluted fractions containing saturates and aromatics were returned to Pacific Northwest National Laboratory (PNNL), where the solvent was removed via evaporation or physical separation using GC techniques. Characterization and separations provided an understanding of saturate and aromatic content, as well as boiling point ranges for each sample and sample fraction. Samples resulting from SPE were examined using EA-IRMS and gas chromatography combustion IRMS (GC-C-IRMS) analyses. Both approaches suggest that the range in values between end-members can be increased by selecting the paraffinic or aromatic fraction of the end-member or by selecting among individual compounds resulting from GC separation of the paraffinic fractions. Considerable work remains to put these approaches into practice and statistically validate the benefit for using a fraction or individual compound over bulk analysis of a sample. However, initial results suggest that separations provide advantages for samples having blend ratios of less than 10% biogenic blendstocks. 13 C results showed statistically similar biofuel blend results to those obtained at PNNL, although additional work is needed to obtain better reproducibility. Select samples were sent to Los Alamos National Laboratory (LANL) for IRMS measurements and Beta Analytics for AMS measurements. This work suggests that IRMS and AMS yield closely comparable results and in some circumstances, IRMS could serve as a surrogate for AMS. While additional work is needed to better resolve statistical advantages for separations and better show the comparable nature of IRMS and AMS in both the biogenic carbon analysis of bulk chemical classes, initial results from this study suggest that these should be pursued in order to proliferate this approach for quantifying biogenic carbon in transportation fuels to the refinery level, thereby potentially enabling process optimization in co-processing scenarios.

09 BIOMASS FUELS↗
DOE OSTI2023

Large Individual Ion FTICR Measurements from the Mid-1990s Using Reactions for Charge Determination Mass Spectrometry

This article discusses from a personal and present-day perspective the first studies of large highly charged individual molecular ions that were conducted using electrospray ionization (ESI) with Fourier transform ion cyclotron resonance (FTICR) MS in the mid-1990s. These studies are distinguished from current Charge Detection Mass Spectrometry (CDMS) research primarily by their use of individual ion charge state changes due to reactions. Here this work describes the key differences in technologies and methods with present CDMS, and the likely implications of these differences. I also comment on surprising individual ion behavior observed in some measurements involving increases in charge state, as well as their possible basis, and also briefly discuss the potential utility of the reaction-based mass measurement approach used in the context of what might more globally be referred to as ‘Charge Determination Mass Spectrometry’.

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

Online detection of airborne nanoparticle composition with mass spectrometry: Recent advances, challenges, and opportunities

Airborne nanoparticles are receiving growing attention due to their impacts on human health, air quality, and climate. Additionally, there are increasing applications of aerosol-based nanotechnology. Real-time measurement of airborne nanoparticle composition is challenging due to their small masses and the difficulties in effectively separating them from larger particles. Custom-built instruments based on mass spectrometry have been developed for nanoparticle composition, including thermal desorption-based, laser-based, and solution-based techniques. They have significantly promoted the understanding of airborne nanoparticles in the last two decades. However, they are affected by molecular fragmentation, lack of mass-resolving power, incomplete species detection, and difficulties in directly comparing to gas-phase measurements. Recent developments in atmospheric mass spectrometry provide possible solutions. Here, this review presents the potential application of these new advances to real-time measurements of the molecular nanoparticle composition and discusses the associated challenges. Such measurements present opportunities for a more comprehensive view of airborne nanoparticles and their impacts.

47 OTHER INSTRUMENTATION↗
NASA NTRS2008

Effect of Nitrogen Gas on the Lifetime of Carbon Nanotube Field Emitters for Electron-Impact Ionization Mass Spectrometry

The lifetime of a patterned carbon nanotube film is evaluated for use as the cold cathode field emission ionization source of a miniaturized mass spectrometer. Emitted current is measured as a function of time for varying partial pressures of nitrogen gas to explore the robustness and lifetime of carbon nanotube cathodes near the expected operational voltages (70-100 eV) for efficient ionization in mass spectrometry. As expected, cathode lifetime scales inversely with partial pressure of nitrogen. Results are presented within the context of previous carbon nanotube investigations, and implications for planetary science mass spectrometry applications are discussed.

Getty, Stephanie A.↗
DOE OSTI2021

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The impact of gas purity on observed reactivity with NO using inductively coupled plasma tandem mass spectrometry

Interference removal in inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) is strongly dependent on the gas selected for use within the collision/reaction cell. There has been little investigation on the effects that reaction gas impurities may have on the resulting spectra. The reactivity of 60 elements was evaluated using nitric oxide (NO 99.5%) with and without a gas purifier to reduce H 2 O impurities to <100 pptV. Experiments were performed using V, Ce, Tl and Th to investigate the effects of purified NO at various flowrates (0.22–1.49 mL min -1 ). Purified NO was shown to significantly mitigate oxy-hydride interferences, improve total ion sensitivity (notable at high gas flows), and shift product distributions advantageously. The reduction in oxy-hydride species results in a product distribution favoring the major expected products, where signals were shown to increase by an order of magnitude. Reduced background and increased signal for the major expected products provides avenues for improving various analytical applications of ICP-MS/MS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗