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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments 1 offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

Min, Sehong↗
DOE OSTI2026

Single-Particle Isotopic Analysis Using the Liquid Sampling-Atmospheric Pressure Glow Discharge Microplasma Coupled to an Orbitrap Mass Spectrometer

Isotope ratio (IR) determinations on individual particles can provide valuable information relative to the sample, including processing and dating, which could be valuable to geological and nuclear material analysis communities. In comparison to “bulk” measurements, in which all particle information is lost and homogenized within a sample, “particle” measurements allow for fingerprinting and can provide unique insights related to the sample’s nano- and micro- compositions. Furthermore, the complex nature of particles, with potential isobaric interferences from either the matrix or other elements within the same particle, poses a significant analytical challenge for conventional mass spectrometry platforms employed for elemental analysis due to their limited mass resolution. Presented here is the first demonstration of an ultrahigh resolution method for single particle (SP) isotopic analysis using the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma ionization source coupled to an Orbitrap mass spectrometer and FTMS Booster X2T acquisition/processing system. For proof of concept, well-characterized CeO 2 microparticles with a nominal diameter of 1.0 μm were analyzed at a mass resolution of ∼330,000. Important instrumental parameters were optimized to enable the detection of single particles. The 142 Ce/ 140 Ce ratio of individual particles and the population average were determined and compared to an SP inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) analysis. The isotopic accuracy and precision were determined by two methods and found to be in good agreement with the SP-ICP-TOF-MS method, with the linear regression slope method providing a more accurate ratio, showing a ∼1.4% relative difference from the ratio determined from a particle digest. The encouraging performance of the method was further supported by a determined detection limit of 2.9 fg ( 142 Ce). The developed method is anticipated to overcome many of the challenges posed by isobaric interferences encountered in conventional mass spectrometry techniques when analyzing real-world samples for particle isotopic composition.

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

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer

Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI–FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. Furthermore, a 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Multimodal Broadband Vibrational Sum Frequency Generation (MM-BB-V-SFG) Spectrometer and Microscope

A broadband sum frequency generation (BB-SFG) spectrometer with multimodal (MM) capabilities was constructed, which could be routinely reconfigured for tabletop experiments in reflection, transmission, and total internal reflection (TIR) geometries, as well as microscopic imaging. The system was constructed using a Ti:sapphire amplifier (800 nm, pulse width = 85 fs, repetition rate = 2 kHz), an optical parameter amplification (OPA) system for production of broadband IR pulses tunable between 1000 and 4000 cm –1 , and two Fabry–Pérot etalons arranged in series for production of narrowband 800 nm pulses. The key feature allowing the MM operation was the nearly collinear alignment of the visible (fixed, 800 nm) and infrared (tunable, 1000–4000 cm –1 ) pulses which were spatially separated. Physical insights discussed in this paper include the comparison of spectral bandwidth produced with 40 and 85 fs pump beams, the improvement of spectral resolution using etalons, the SFG probe volume in bulk analysis, the normalization of SFG signals, the stitching of multiple spectral segments, and the operation in different modes for air/liquid and adsorbate/solid interfaces, bulk samples, as well as spectral imaging combined with principle component analysis (PCA). Finally, the SFG spectral features obtained with the MM-BB-SFG system were compared with those obtained with picosecond-scanning-SFG system and high-resolution BB-SFG system (HR-BB-SFG) for dimethyl sulfoxide, α-pinene, and various samples containing cellulose (purified commercial products, Cladophora cell wall, cotton and flax fibers, and onion epidermis cell wall).

47 OTHER INSTRUMENTATION↗
DOE OSTI2012

Bio-oil Analysis Using Negative Electrospray Ionization: Comparative Study of High-Resolution Mass Spectrometers and Phenolic versus Sugaric Components

Here we have previously demonstrated that a petroleomic analysis could be performed for bio-oils and revealed the complex nature of bio-oils for the nonvolatile phenolic compounds. As a subsequent study, we have adapted electrospray ionization in negative-ion mode to characterize a wide variety of bio-oil compounds. A comparative study of three common high-resolution mass spectrometers was performed to validate the methodology and to investigate the differences in mass discrimination and resolution. The mass spectrum is dominated by low mass compounds with m/z of 100–250, with some compounds being analyzable by gas chromatography–mass spectrometry (GC–MS). We could characterize over 800 chemical compositions, with only about 40 of them being previously known in GC–MS. This unveiled a much more complex nature of bio-oils than typically shown by GC–MS. The pyrolysis products of cellulose and hemicellulose, particularly polyhydroxy cyclic hydrocarbons (or what we call “sugaric” compounds), such as levoglucosan, could be effectively characterized with this approach. Phenolic compounds from lignin pyrolysis could be clearly distinguished in a contour map of double bond equivalent (DBE) versus the number of carbons from these sugaric compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Bayesian Model for HOPE Mass Spectrometers on Van Allen Probes

Space instruments rely heavily on modeling to predict and understand the instrument response, enabling a determination of the capabilities and resolution. The Bayesian approach provides a framework to incorporate prior knowledge and propagate uncertainty to predict the instrument response. We present an empirical Bayes model for the end-to-end performance of the Helium, Oxygen, Proton, and Electron mass spectrometers aboard the Van Allen Probes mission. In this model, we use a combination of external modeling, laboratory calibration, and expert opinion to construct the time-of-flight spectra and demonstrate good agreement with on-orbit data. The empirical Bayes model is applied to explore doubly charged ions and carbon, nitrogen, oxygen discrimination during the Van Allen Probes mission.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Comprehensive Characterization of Water Group Ion Composition and Distributions in Saturn's Magnetosphere With Cassini Plasma Spectrometer Data

Saturn's magnetosphere is continuously supplied with neutrals from the Enceladus plume and the icy rings, which undergo ionization and charge-exchange to form a complex water-group plasma environment. While the Cassini Plasma Spectrometer (CAPS) instrument has provided extensive compositional information, detailed separation of individual water-group ion species in time-of-flight (TOF) data has not previously been achieved. In this study, we perform forward modeling of CAPS-IMS energy-per-charge (E/Q) and TOF spectra obtained between 2004 and 2012 to resolve O + , OH + , H 2 O + , and H 3 O + and to characterize their plasma properties, including number density, temperature, and thermodynamic κ. Our results demonstrate that O + is the dominant thermal ion species throughout Saturn's magnetosphere, comprising up to ∼70% of the total ion population beyond ∼5 Saturn radii (R S ). In contrast, molecular ions such as OH + , H 2 O + , and H 3 O + dominate closer to Enceladus but rapidly dissociate into atomic ions between ∼5 and 10 R S . This radial region is also characterized by the steepest increase in plasma flow speed, which rises from ∼40% to ∼80% of rigid corotation. Simultaneously, ion velocity distributions approach Maxwell–Boltzmann equilibrium, as indicated by high kappa values. These findings provide new constraints on the ion–neutral chemistry that regulates the balance between molecular and atomic ions in Saturn's magnetosphere. They also emphasize the critical role of the 5–10 R S region as a transition zone for both plasma composition and dynamics. Our results refine previous CAPS-based studies and underscore the need to incorporate seasonal variability and ionospheric coupling into future global models of Saturn's plasma environment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Test of the GEM Front Tracker for the SBS Spectrometer at Jefferson Lab

A new Large-Acceptance Forward Angle Spectrometer (Super BigBite) is under development at JLab/Hall A to optimally exploit the exciting opportunities o?ered by the 12 GeV upgrade of the electron beam. The tracker of this new apparatus is based on the Gas Electron Multiplier (GEM) technology, which has been chosen to optimize cost/performance, position resolution and to meet the high hit rate (>1 MHz/cm2). The first GEM detector modules, designed and built by the INFN Collaboration JLAB12, were tested at the DESY test beam facility in Hamburg, by using an electron beam with energy ranging from 2.0 to 6.0 GeV. In particular, two 40x50 cm2 and one 10x10 cm2 GEM chambers were equipped with a new implementation of the APV25 readout chip. Measurements were performed at di?erent impact points and angles between the electron beam and the plane of the GEM chambers, with one large chamber in a solenoid magnetic field up to 500 Gauss. In this report we present the technical characteristics of the detector and comment on the presently achieved performance.

Mammoliti, F.↗
DOE OSTI2015

Extracting source parameters from beam monitors on a chopper spectrometer

The intensity distributions of beam monitors in direct-geometry time-of-flight neutron spectrometers provide important information about the instrument resolution. For short-pulse spallation neutron sources in particular, the asymmetry of the source pulse may be extracted and compared to Monte Carlo source simulations. An explicit formula using a Gaussian-convolved Ikeda-Carpenter distribution is given and compared to data from the ARCS instrument at the Spallation Neutron Source.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Analysis of the time-of-flight neutron scattering cross-section data for light water measured at the SEQUOIA spectrometer, Spallation Neutron Source (SNS)

Thermal neutron scattering cross-section data for light water available in the major nuclear data libraries observes significant differences especially at reactor operating temperatures. During the past few years there has been a renewed interest in reviewing the existing thermal scattering models and generating more accurate and reliable thermal scattering cross sections using existing experimental data and in some cases based on Molecular Dynamics (MD) simulations. There is a need for performing new time-of-flight experiments at high temperatures and pressures, to have a better understanding of the physics involved in the scattering process that could help improve the existing TSL data.Lack of experimental thermal scattering data for light water at high temperatures led to a new measurement campaign within the INSIDER project at the Institut de radioprotection et de sûreté nucléaire (IRSN). Double differential scattering cross section for light water have been measured at the SEQUOIA spectrometer based at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, United States. Several measurements have been carried out at different temperatures and pressures corresponding to liquid light water. Measurements at five different incident neutron energies Ei (8, 60, 160, 280 and 800 meV) have been carried out to help exploring different regions of the frequency spectrum. This paper presents the analysis of the dynamic structure factor and the derived frequency spectrum of light water. The analysis of the experimental data would provide one with better confidence, the behavior of thermal scattering cross sections for light water at high temperatures, knowledge of which is very important for the design of novel reactors as well as existing pressurized water reactors.

Jaiswal, V↗
DOE OSTI2023

Thermal scattering law for ice based on neutron time-of-flight experiments carried out at the SEQUOIA spectrometer at the Oak Ridge National Laboratory

Precise estimation of neutron thermalization in moderators relies on high-fidelity thermal scattering cross-section data governed by the thermal scattering law (TSL). The Institut de Radioprotection et de Sûreté Nucléaire (IRSN) has been working on the development of improved TSL for light water ice. Many polymorphic phases of light water ice exist depending on the thermodynamic conditions. The most common type of ice at standard pressure and temperature below water freezing point (273.15 K) is ice-Ih. It is essential to have high-resolution experimental double differential data for developing and/or validating TSL for moderator materials.Existing experimental double-differential scattering data for ice-Ih are extremely sparse and of limited quality. New high-quality double-differential measurements for ice-Ih over multiple temperatures and incident neutron energies would directly support the validation and improvement of ice-Ih TSL models for criticality safety applications.Series of time-of-flight (TOF) inelastic neutron scattering experiments on ice-Ih at temperatures starting at 271 K and down to 6 K, have been carried out at the SEQUOIA spectrometer at the Spallation Neutron Source (SNS) at the Oak Ridge National Laboratory (ORNL), United States. The experiments have been performed for incident neutron energies, Ei= 11, 55, 160, 250, and 600 meV, to explore different excitation energies in the vibrational phonon spectrum. This paper presents the thermodynamic conditions and the details of the TOF measurements on ice-Ih and the derived phonon spectrum from the experimentally measured double differential data. A study of the variation of the phonon spectrum of ice-Ih as a function of temperature is highlighted, and a preliminary TSL evaluation is developed based on the experimental phonon spectrum.

Jaiswal, V↗
DOE OSTI2016

The cold neutron chopper spectrometer at the Spallation Neutron Source—A review of the first 8 years of operation

The first eight years of operation of the Cold Neutron Chopper Spectrometer (CNCS) at the Spallation Neutron Source in Oak Ridge is being reviewed. The instrument has been part of the facility user program since 2009, and more than 250 individual user experiments have been performed to date. CNCS is an extremely powerful and versatile instrument and offers leading edge performance in terms of beam intensity, energy resolution, and flexibility to trade one for another. In addition, experiments are being routinely performed with the sample at extreme conditions: T ≲ 0.05 K, p ≳ 2 GPa, and B = 8 T can be achieved individually or in combination. In particular, CNCS is in a position to advance the state of the art with inelastic neutron scattering under pressure, and some of the recent accomplishments in this area will be presented in more detail.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Imaging crystal spectrometer for high-resolution x-ray measurements on electron beam ion traps and tokamaks

Here, we describe a crystal spectrometer implemented on the Livermore electron beam ion traps that employ two spherically bent quartz crystals and a cryogenically cooled back-illuminated charge-coupled device detector to measure x rays with a nominal resolving power of λ/Δλ ≥ 10 000. Its focusing properties allow us to record x rays either with the plane of dispersion perpendicular or parallel to the electron beam and, thus, to preferentially select one of the two linear x-ray polarization components. Moreover, by choice of dispersion plane and focussing conditions, we use the instrument either to image the distribution of the ions within the 2 cm long trap region, or to concentrate x rays of a given energy to a point on the detector, which optimizes the signal-to-noise ratio. We demonstrate the operation and utility of the new instrument by presenting spectra of Mo 34+ , which prepares the instrument for use as a core impurity diagnostic on the NSTX-U spherical torus and other magnetic fusion devices that employ molybdenum as plasma facing components.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

High resolution, high signal-to-noise crystal spectrometer for measurements of line shifts in high-density plasmas

The Orion high-resolution x-ray (OHREX) spectrometer has been a successful tool for measuring the shapes of density-broadened spectral lines produced in short-pulse heated plasmas at the Orion laser facility. We have recently outfitted the instrument with a charge-couple device (CCD) camera, which greatly increased the accuracy with which we can perform line-shift measurements. Because OHREX is located on the outside of the Orion target chamber, no provisions for the shielding of electromagnetic pulses are required. With the CCD, we obtained a higher signal-to-noise ratio than we previously obtained with an image-plate detector. As a result, this allowed us to observe structure in the image produced by the diffraction from the two OHREX crystals, which was highly reproducible from shot to shot. This structure will ultimately limit the accuracy of our spectroscopic measurements

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

Micro-spectrometer for fusion plasma boundary measurements

In situ probes are being developed to make direct, spatially resolved measurements of the ion energy spectra in the edge of tokamak plasmas while being easily replaced and requiring minimal resources. The ion spectrometers will consist of a combined collimator and energy analyzer fabricated from silicon and mated to a detector to yield a form factor of approximately 2.0 cm × 1.5 cm × 0.2 cm. Results of fabrication and testing of the combined collimator and energy analyzer element are presented.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

High-energy differential-filtering photon spectrometer for ultraintense laser-matter interactions

Large quantities of ultrahigh-energy x-rays are produced by petawatt-class lasers; however, spectroscopy in this range of 0.1-1 MeV is difficult due to the long photon mean free path. A novel geometry step filter to measure the high-energy bremsstrahlung emission tail has been developed for use in high energy density, short-pulse laser-matter interaction experiments. The grid design of the filters allows for the independent determination of a local background, which reduces systematic errors in the reconstructed spectra. This spectrometer was used to measure x-ray spectra for various laser and target conditions at intensities near 1 × 10 18 W/cm 2 where single-exponential bremsstrahlung spectra were fit to the data and show an increasing photon temperature with pulse duration for a fixed laser intensity.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

An improved laboratory-based x-ray absorption fine structure and x-ray emission spectrometer for analytical applications in materials chemistry research

X-ray absorption fine structure (XAFS) and x-ray emission spectroscopy (XES) are advanced x-ray spectroscopies that impact a wide range of disciplines. Furthermore, unlike the majority of other spectroscopic methods, XAFS and XES are accompanied by an unusual access model, wherein the dominant use of the technique is for premier research studies at world-class facilities, i.e., synchrotron x-ray light sources. In this paper, we report the design and performance of an improved XAFS and XES spectrometer based on the general conceptual design of Seidler et al. [Rev. Sci. Instrum. 85, 113906 (2014)]. New developments include reduced mechanical degrees of freedom, much-increased flux, and a wider Bragg angle range to enable extended x-ray absorption fine structure (EXAFS) measurement and analysis for the first time with this type of modern laboratory XAFS configuration. This instrument enables a new class of routine applications that are incompatible with the mission and access model of the synchrotron light sources. To illustrate this, we provide numerous examples of x-ray absorption near edge structure (XANES), EXAFS, and XES results for a variety of problems and energy ranges. Highlights include XAFS and XES measurements of battery electrode materials, EXAFS of Ni with full modeling of results to validate monochromator performance, valence-to-core XES for 3d transition metal compounds, and uranium XANES and XES for different oxidation states. Taken en masse , these results further support the growing perspective that modern laboratory-based XAFS and XES have the potential to develop a new branch of analytical chemistry.

47 OTHER INSTRUMENTATION↗