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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Cryo-EM sample preparation for high-resolution structure studies

High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. Here, in this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform

Conventional proteomics measures the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of significant changes in subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot precisely infer the abundance changes of intact proteins, which are presented as proteoforms. Herein, we described a spatially resolved top-down proteomics (TDP) platform for proteoform identification and quantification directly on thin tissue sections. The spatial TDP platform consisted of a nanoPOTS (nanodroplet Processing in One pot for Trace Samples)-based sample preparation system and an LCM (laser capture microdissection)-based cell isolation system. We improved the nanoPOTS sample preparation by adding benzonase in the extraction buffer to enhance the coverage of nucleus proteins. Using ~200 cultured cells as model samples, the improved approach increased proteoform identifications from 493 to 700; newly identified proteoforms primarily corresponded to nuclear proteins. To demonstrate the spatial TDP platform in tissue samples, we analyzed LCM-isolated tissue voxels from rat brain cortex and hypothalamus regions. We quantified 426 proteoforms by combining identifications from TopPIC and TDPortal with the quantitation from ProMex. Several proteoforms corresponding to the same gene exhibited mixed abundance profiles between two tissue regions, suggesting potential PTM-specific spatial distributions. The spatial TDP workflow has prospects for biomarker discovery at proteoform level from small tissue sections.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

New Methods of Sample Preparation for Atom Probe Specimens

Magnetite is a common conductive mineral found on Earth and Mars. Disk-shaped precipitates approximately 40 nm in diameter have been shown to have manganese and aluminum concentrations. Atom-probe field-ion microscopy (APFIM) is the only technique that can potentially quantify the composition of these precipitates. APFIM will be used to characterize geological and planetary materials, analyze samples of interest for geomicrobiology; and, for the metrology of nanoscale instrumentation. Prior to APFIM sample preparation was conducted by electropolishing, the method of sharp shards (MSS), or Bosch process (deep reactive ion etching) with focused ion beam (FIB) milling as a final step. However, new methods are required for difficult samples. Many materials are not easily fabricated using electropolishing, MSS, or the Bosch process, FIB milling is slow and expensive, and wet chemistry and the reactive ion etching are typically limited to Si and other semiconductors. APFIM sample preparation using the dicing saw is commonly used to section semiconductor wafers into individual devices following manufacture. The dicing saw is a time-effective method for preparing high aspect ratio posts of poorly conducting materials. Femtosecond laser micromachining is also suitable for preparation of posts. FIB time required is reduced by about a factor of 10 and multi-tip specimens can easily be fabricated using the dicing saw.

rock varnish↗
DOE OSTI2025

Site-specific plan-view (S)TEM sample preparation from thin films using a dual-beam FIB-SEM

To fully evaluate the atomic structure, and associated properties of materials using transmission electron microscopy, examination of samples from three non-collinear orientations is needed. This is particularly challenging for thin films and nanoscale devices built on substrates due to limitations with plan-view sample preparation. In this work, a new method for preparation of high-quality, site-specific, plan-view TEM samples from thin-films grown on substrates, is presented and discussed. Here, it is based on using a dual-beam focused ion beam scanning electron microscope (FIB-SEM) system. To demonstrate the method, the samples were prepared from thin films of perovskite oxide BaSnO 3 grown on a SrTiO 3 substrate and metal oxide IrO 2 on a TiO 2 substrate, ranging from 20–80 nm in thicknesses using molecular beam epitaxy. While the method is optimized for the thin films, it can be extended to other site-specific plan-view samples and devices build on wafers. Aberration-corrected STEM was used to evaluate the quality of the samples and their applicability for atomic-resolution imaging and analysis.

BaSnO3↗
DOE OSTI2023

Sample Preparation Method for Low-Level Total 129 I Measurements by ICP-MS

Trace-level measurements of iodine’s isotopic ( 129 I and 127 I) and chemical species distributions are needed for an accurate understanding of radioiodine migration in the Hanford subsurface. Pacific Northwest National Laboratory (PNNL) previously developed a novel analytical method for iodine characterization that uses ion chromatography (IC) coupled to inductively coupled mass spectrometry (ICP-MS). While the method can measure speciated forms of 129 I at levels below the drinking water standard, an interference from molybdenum (Mo) prevents the assay from quantifying the $\underline{total}$ 129 I concentration in many Hanford sample matrices. In this work, solvent extraction was evaluated as a sample preparation method for eliminating the Mo interference. A series of 10 experiments was conducted in which solutions containing known amounts of iodate or iodide were treated by solvent extraction, and the extracted solutions were analyzed for total iodine concentrations by ICP MS. Several extraction parameters such as reagent concentrations and chemical reaction times were systematically adjusted in attempts to optimize the extraction process. While solvent extraction was shown to be effective at removing Mo, there was a consistent inability to recover more than approximately 75% of the total iodine in most experiments. This would reduce the ability to detect 129 I at levels near the drinking water standard. Additionally, the extraction efficiencies in several experiments were highly variable, suggesting that solvent extraction could add significant uncertainty to radioiodine measurements. We recommend evaluating ion exchange as an alternative sample preparation approach in fiscal year (FY) 2024.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Aggregated nanoparticles: Sample preparation and analysis by atom probe tomography

Atom probe tomography (APT) allows measurement of the three-dimensional structure and composition of materials, but specific sample preparation procedures are required for challenging materials such as aggregates of nanoparticles. Indeed, the presence of porosity within the specimen affects both the stability of the sample and the accuracy of the data. In this work, aggregates of nanoparticles were transferred onto a micromanipulator tip and embedded via electron-beam-assisted deposition of Pt. Successive FIB-millings and Pt-depositions are needed to create suitable APT tips. The 3D reconstruction reveals the presence of 15–20 nm nanoparticles, and massspectral analysis shows the absence of trace elements within the catalyst, thus serving as quality control for the synthesis of nanoparticles with specific compositions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRS2010

Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.

Gendreau, Keith↗
DOE OSTI2020

Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells

Protein analysis of small numbers of human cells is primarily achieved by targeted proteomics with antibody-based immunoassays, which have inherent limitations (e.g., low multiplex and unavailability of antibodies for new proteins). Mass spectrometry (MS)-based targeted proteomics has emerged as an alternative because it is antibody-free, high multiplex, and has high specificity and quantitation accuracy. Recent advances in MS instrumentation make MS-based targeted proteomics possible for multiplexed quantification of highly abundant proteins in single cells. However, there is a technical challenge for effective processing of single cells with minimal sample loss for MS analysis. To address this issue, we have recently developed a convenient protein carrier-assisted one-pot sample preparation coupled with liquid chromatography (LC) - selected reaction monitoring (SRM) termed cLC-SRM for targeted proteomics analysis of small numbers of human cells. This method capitalizes on using the combined excessive exogenous protein as a carrier and low-volume one-pot processing to greatly reduce surface adsorption losses as well as high-specificity LC-SRM to effectively address the increased dynamic concentration range due to the addition of exogeneous carrier protein. Its utility has been demonstrated by accurate quantification of most moderately abundant proteins in small numbers of cells (e.g., 10-100 cells) and highly abundant proteins in single cells. The easy-to-implement features and no need for specific devices make this method readily accessible to most proteomics laboratories. In this study, we have provided a detailed protocol for cLC-SRM analysis of small numbers of human cells including cell sorting, cell lysis and digestion, LC-SRM analysis, and data analysis. Further improvements in detection sensitivity and sample throughput are needed towards targeted single-cell proteomics analysis. We anticipate that cLC-SRM will be broadly applied to biomedical research and systems biology with the potential of facilitating precision medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Hanging drop sample preparation improves sensitivity of spatial proteomics

Spatial proteomics holds great promise for revealing tissue heterogeneity in both physiological and pathological conditions. However, one significant limitation of most spatial proteomics workflows is the requirement of large sample amounts that blurs cell-type-specific or microstructure-specific information. In this study, we developed an improved sample preparation approach for spatial proteomics and integrated it with our previously-established laser capture microdissection (LCM) and microfluidics sample processing platform. Specifically, we developed a hanging drop (HD) method to improve the sample recovery by positioning a nanowell chip upside-down during protein extraction and tryptic digestion steps. Compared with the commonly-used sitting-drop method, the HD method keeps the tissue pixel away from the container surface, and thus improves the accessibility of the extraction/digestion buffer to the tissue sample. The HD method can increase the MS signal by 7 fold, leading to a 66% increase in the number of identified proteins. An average of 721, 1489, and 2521 proteins can be quantitatively profiled from laser-dissected 10 μm-thick mouse liver tissue pixels with areas of 0.0025, 0.01, and 0.04 mm 2 , respectively. The improved system was further validated in the study of cell-type-specific proteomes of mouse uterine tissues.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Sputter sample preparation for ion beam delivery of radium-223 at ATLAS

A radium-223 ion beam was delivered to an experiment from the electron cyclotron resonance ion source, ECR2, at the Argonne Tandem Linac Accelerator System (ATLAS). Here, the radium-223 material was in a nitrate salt form within a vial, prior to being converted to a usable sputter sample. The sputter sample was produced using a new sample preparation method, where the radium nitrate was dissolved into a solution and pipetted onto pressed aluminum powder. This sample was then allowed to dry, distributing the radium-223 material throughout the sputter sample. Ion source operation using the radium sputter sample is described with the operating parameters listed. The intensity and energy requirements for this ion beam were 1 × 10 6 particles/s and 1.07 GeV, respectively. Because the intensity is relatively low compared to most experiments at ATLAS, previously developed accelerator mass spectrometry methods were used Scott et al. to avoid the need for tuning of the low-intensity beam of interest. Handling of the radium material, as well as loading and unloading of the sputter sample from ECR2, required collaboration with Health Physics. Procedures were used and dry runs were carried out before, during, and after the experiment to ensure the safety of the workers. The processes used and lessons learned are described within.

07 ISOTOPE AND RADIATION SOURCES↗
NASA NTRS1992

Glass sample preparation and performance investigations

This final report details the work performed under this delivery order from April 1991 through April 1992. The currently available capabilities for integrated optical performance modeling at MSFC for large and complex systems such as AXAF were investigated. The Integrated Structural Modeling (ISM) program developed by Boeing for the U.S. Air Force was obtained and installed on two DECstations 5000 at MSFC. The structural, thermal and optical analysis programs available in ISM were evaluated. As part of the optomechanical engineering activities, technical support was provided in the design of support structure, mirror assembly, filter wheel assembly and material selection for the Solar X-ray Imager (SXI) program. As part of the fabrication activities, a large number of zerodur glass samples were prepared in different sizes and shapes for acid etching, coating and polishing experiments to characterize the subsurface damage and stresses produced by the grinding and polishing operations. Various optical components for AXAF video microscope and the x-ray test facility were also fabricated. A number of glass fabrication and test instruments such as a scatter plate interferometer, a gravity feed saw and some phenolic cutting blades were fabricated, integrated and tested.

Johnson, R. Barry↗
DOE OSTI2026

Sample Preparation Laboratory (SPL) Best Practices: CGD as the Primary Acceptance Method

The traditional paradigm applied to the construction of nuclear safety related systems, structures, and components (SSCs), like SPL, involves an owner/licensee hiring an EPC firm with an NQA 1 program to manage the engineering, procurement, and construction of the desired SSC. This traditional approach would have posed significant barriers to the successful completion of the SPL. As a smaller capital project, in the $\$$100–$\$$200 million range, there was concern that employing one of the larger EPC companies would escalate costs and extend the projected schedule beyond what would be feasible for the Department of Energy (DOE). The traditional acceptance method employed for nuclear facilities with credited safety functions requires the use of an EPC firm applying American Society of Mechanical Engineers (ASME) NQA 1 nuclear quality assurance (NQA) to accept safety SSCs. In lieu of this approach, INL elected to apply its own NQA 1 program to hire an EPC firm operating a commercial quality program. This method used commercial grade dedication (CGD) as outlined in NQA 1 which had not been applied at this scale. Use of the commercial supply chain was identified as a key factor to the successful completion of SPL. Favorable conditions enabling the use of CGD included: • INL serving as both the designer and the design authority • Design created by an NQA 1 qualified source • A mature CGD program • Availability of a CGD subject matter expert (SME) • A strong construction management program. This white paper elaborates on the methodology employed in the construction of the SPL, the successes achieved, and best practices implemented.

42 - ENGINEERING↗
NASA NTRS1979

Paleointensity determinations at elevated temperatures - Sample preparation technique

A technique has been developed for the encapsulation of rock samples in order to prevent the chemical alterations which commonly accompany paleointensity measurements at elevated temperatures. The technique involves vacuum pumping at about 100 C of the sample as placed in a silica tube. The tube containing the sample and a Ti 'getter' are sealed under vacuum. Measurements can be made at 200 and 300 C. Immediately after this, the sample is sealed-off from the getter. The sample is now ready for measurements at higher temperatures.

Taylor, L. A.↗
NASA NTRS1974

Preservation of lunar core samples - Preparation and interpretation of three-dimensional stratigraphic sections

Preservation and analysis of core samples collected from the lunar regolith are discussed. The objectives of core sampling are described together with the core-sampling equipment used in the Apollo program. The effects of disaggregation in core samples are summarized, and ways to preserve the stratigraphy in these samples are reviewed, particularly partial impregnation of samples with polybutyl methacrylate. It is shown that stratigraphic sections preserved in this way reveal individual fragments of the regolith in their original positions, primary and secondary depositional structures related to lunar processes, and the nature and extent of deformations caused by sampling equipment. It is concluded that since the core sedimentary structures indicate complex three-dimensional variations in the regolith, quantitative models of regolith evolution must allow for distinctive local histories as well as irregular reworking and deposition events due to impact processes.

Fryxell, R.↗
NASA NTRS1992

OSEE responses on D6AC steel due to sample preparation

A cleaning procedure and a contamination method developed at NASA Langley to contaminate sample surfaces with a certain thickness of HD-2 grease are demonstrated. Varying levels of contamination are obtained. Optically stimulated electron emission (OSEE) measurements were performed using the parallel electric field cell and the Pat scan device for clean and contaminated samples with a known amount of common contaminant. The OSEE response is found to be more sensitive for the clean sample than for the contaminated one. It is concluded that the OSEE measurements obtained using these techniques are sensitive to surface conditions and the contaminant thickness variations. It is also shown that the wavelength of illuminating light can have a profound effect on OSEE current levels.

Abedin, M. N.↗
NASA NTRS2010

Preview of the NASA NNWG NDE Sample Preparation Handbook

This viewgraph presents a step-by-step how-to fabrication documentation of every kind of sample that is fabricated for MSFC by UA Huntsville, including photos and illustrations. The tabulation of what kind of samples are being fabricated for what NDE method, detailed instructions/documentation of the inclusion/creation of defects, detailed specifications for materials, processes, and equipment, case histories and/or experiences with the different fabrication methods and defect inclusion techniques, discussion of pitfalls and difficulties associated with sample fabrication and defect inclusion techniques, and a discussion of why certain fabrication techniques are needed as related to the specific NDE methods are included in this presentation.

Source record↗