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NASA NTRS1999

Acoustic Treatment Design Scaling Methods: Analytical and Experimental Data Correlation - Volume 5

The primary purpose of the study presented in this volume is to present the results and data analysis of in-duct transmission loss measurements. Transmission loss testing was performed on full-scale, 1/2-scale, and 115-scale treatment panel samples. The objective of the study was to compare predicted and measured transmission loss for full-scale and subscale panels in an attempt to evaluate the variations in suppression between full- and subscale panels which were ostensibly of equivalent design. Generally, the results indicated an unsatisfactory agreement between measurement and prediction, even for full-scale. This was attributable to difficulties encountered in obtaining sufficiently accurate test results, even with extraordinary care in calibrating the instrumentation and performing the test. Test difficulties precluded the ability to make measurements at frequencies high enough to be representative of subscale liners. It is concluded that transmission loss measurements without ducts and data acquisition facilities specifically designed to operate with the precision and complexity required for high subscale frequency ranges are inadequate for evaluation of subscale treatment effects.

Chien, W. E.↗

NASA NTRS2012

Carbon and Hydrogen Isotope Measurements of Alcohols and Organic Acids by Online Pyroprobe-GC-IRMS

The detection of methane in the atmosphere of Mars, combined with evidence showing widespread water-rock interaction during martian history, suggests that the production of methane on Mars may be the result of mineral surface-catalyzed CO2 and or CO reduction during Fisher-Tropsch Type (FTT) reactions. A better understanding of these reaction pathways and corresponding C and H isotope fractionations is critical to deciphering the synthesis of organic compounds produced under abiotic hydrothermal conditions. Described here is a technique for the extraction and analysis of both C and H isotopes from alcohols (C1-C4) and organic acids (C1-C6). This work is meant to provide a "proof of concept" for making meaningful isotope measurements on complex mixtures of solid-phase hydrocarbons and other intermediary products produced during high-temperature and high-pressure synthesis on mineral-catalyzed surfaces. These analyses are conducted entirely "on-line" utilizing a CDS model 5000 Pyroprobe connected to a Thermo Trace GC Ultra that is interfaced with a Thermo MAT 253 isotope ratio mass spectrometer operating in continuous flow mode. Also, this technique is designed to carry a split of the GC-separated product to a DSQ II quadrupole mass spectrometer as a means of making semi-quantitative compositional measurements. Therefore, both chemical and isotopic measurements can be carried out on the same sample.

Socki, Richard A.↗

DOE OSTI2019

Literature Review of Generalized Two-Dimensional Correlation Spectroscopy (2D-COS)

Generalized two-dimensional correlation spectroscopy (2D-COS) is a technique that has improved on traditional spectroscopic techniques by exposing samples to a variable amount of an external perturbation before they have been probed spectroscopically through IR, UV, Raman, etc. These perturbed signals are plotted over a second independent wavenumber axis and after mathematical manipulation, a dynamic spectrum is created that shows the synchronous and asynchronous spectra. The dynamic spectrum shows the way spectral changes in the material are correlated to each other, and a mechanism of material degradation can be proposed through a set of rules that Noda proposed. This technique is important to spectroscopic studies because of improved spectral resolution and the identification of complex or overlapping bands that cannot be distinguished in traditional analytical methods. This technique has been widely utilized since its inception, and has developed towards protein studies, as well as even wine chemistry, because of the advanced capabilities of band separation. Two-dimensional hetero-spectral correlation analysis has also been developed to find correlations in spectra with different spectroscopic probes. 2D-COS as an analytical technique has increasing avenues of expansion, and can be creatively used in many other fields in the future.

2D-COS↗

DOE OSTI2022

Enzymatic Laser-Induced Graphene Biosensor for Electrochemical Sensing of the Herbicide Glyphosate

Glyphosate is a globally applied herbicide yet it has been relatively undetectable in-field samples outside of gold-standard techniques. Its presumed nontoxicity toward humans has been contested by the International Agency for Research on Cancer, while it has been detected in farmers’ urine, surface waters and crop residues. Rapid, on-site detection of glyphosate is hindered by lack of field-deployable and easy-to-use sensors that circumvent sample transportation to limited laboratories that possess the equipment needed for detection. Herein, the flavoenzyme, glycine oxidase, immobilized on platinum-decorated laser-induced graphene (LIG) is used for selective detection of glyphosate as it is a substrate for GlyOx. The LIG platform provides a scaffold for enzyme attachment while maintaining the electronic and surface properties of graphene. The sensor exhibits a linear range of 10–260 µm, detection limit of 3.03 µm, and sensitivity of 0.991 nA µm -1 . The sensor shows minimal interference from the commonly used herbicides and insecticides: atrazine, 2,4-dichlorophenoxyacetic acid, dicamba, parathion-methyl, paraoxon-methyl, malathion, chlorpyrifos, thiamethoxam, clothianidin, and imidacloprid. Sensor function is further tested in complex river water and crop residue fluids, which validate this platform as a scalable, direct-write, and selective method of glyphosate detection for herbicide mapping and food analysis.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Characteristics of the Diffuse Astrophysical Electron and Tau Neutrino Flux with Six Years of IceCube High Energy Cascade Data

In this work, we report on the first measurement of the astrophysical neutrino flux using particle showers (cascades) in IceCube data from 2010-2015. Assuming standard oscillations, the astrophysical neutrinos in this dedicated cascade sample are dominated (~90%) by electron and tau flavors. The flux, observed in the sensitive energy range from 16 TeV to 2.6 PeV, is consistent with a single power-law model as expected from Fermi-type acceleration of high energy particles at astrophysical sources. We find the flux spectral index to be γ=2.53±0.07 and a flux normalization for each neutrino flavor of $\phi$ astro =1.66$_{-0.27}^{+0.25}$ at E 0 =100 TeV, in agreement with IceCube's complementary muon neutrino results and with all-neutrino flavor fit results. In the measured energy range we reject spectral indices γ≤2.28 at ≥3σ significance level. Because of high neutrino energy resolution and low atmospheric neutrino backgrounds, this analysis provides the most detailed characterization of the neutrino flux at energies below ~100 TeV compared to previous IceCube results. Results from fits assuming more complex neutrino flux models suggest a flux softening at high energies and a flux hardening at low energies (p value ≥0.06). The sizable and smooth flux measured below ~100 TeV remains a puzzle. In order to not violate the isotropic diffuse gamma-ray background as measured by the Fermi Large Area Telescope, it suggests the existence of astrophysical neutrino sources characterized by dense environments which are opaque to gamma rays.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

A rapid thioacidolysis method for biomass lignin composition and tricin analysis

Abstract Background Biomass composition varies from plant to plant and greatly affects biomass utilization. Lignin is a heterogeneous phenolic polymer derived mainly from p -coumaryl, coniferyl, and sinapyl alcohols and makes up to 10–25% of lignocellulosic biomass. Recently, tricin, an O -methylated flavone, was identified as a lignin monomer in many grass species. Tricin may function as a nucleation site for lignification and is advocated as a novel target for lignin engineering to reduce lignin content and improve biomass digestibility in grasses. Thioacidolysis is an analytical method that can be adapted to analyze both lignin monomeric composition and tricin content in the lignin polymer. However, the original thioacidolysis procedure is complex, laborious, and time consuming, making it difficult to be adopted for large-scale screening in biomass research. In this study, a modified, rapid higher throughput thioacidolysis method was developed. Results In combination with gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS), the modified thioacidolysis method can be used to simultaneously characterize the lignin composition and tricin content using 2–5 mg of dry samples. The modified method eliminates the solvent extraction and drastically improves the throughput; 80 samples can be processed in one day per person. Our results indicate that there is no significant difference in the determination of lignin S/G ratio and tricin content between the original and modified methods. Conclusions A modified thioacidolysis protocol was established. The results demonstrate that the modified method can be used for rapid, high-throughput, and reliable lignin composition and tricin content analyses for screening transgenic plants for cell wall modifications or in large-scale genome-wide association studies (GWAS).

09 BIOMASS FUELS↗

DOE OSTI2019

Microstructural Modeling of the α + β Phase in Ti-6Al-4V: A Diffusion-Based Approach

Complex heat treatment operations and advanced manufacturing processes such as laser or electron-beam welding will see the metallic workpiece experience a considerable range of temperatures and heating/cooling rates. These intrinsic conditions will have a significant bearing upon the microstructure of the material, and in turn upon the thermo-mechanical properties. In this work, a diffusion-based approach to model the growth and shrinkage of precipitates in the alpha + beta field of the common titanium alloy Ti-6Al-4V is established. Further, the numerical model is extended using a JMA-type approach to explore the dependency of the beta-transus temperature on extremely high heating rates, whereby dissolution alone is too slow to accurately describe the alpha to beta-phase transformation. Experimental heat treatments at rates of 5, 50, and 500 °C/s were performed, and metallographic analysis of the samples was used to validate the numerical modeling framework predictions for lamellar shrinkage, while data from the literature has been used to evaluate the numerical modeling framework for the growth of equiaxed microstructures. The agreement between measurements and numerical predictions was found to be good.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Supercritical water desalination and oxidation (SCWDO): Effectiveness on complex solutions, technoeconomic, and CO 2 impact for produced water treatment

The modern energy-economy is increasingly causing the production of highly saline brines, including from produced water. Supercritical water desalination can concentrate and extract minerals from these brines, but the effects of mixed salt interactions, organic degradation with additives, and the technology's economics are not well understood at supercritical condition. The present study evaluated and experimentally studied an integrated supercritical water desalination and oxidation (SCWDO) process for treating real-produced water samples from oil/natural gas field. The complex interactions between the various anions and cations in produced water were extensively evaluated. Most of the divalent and trivalent ions were extracted below 250 °C while the majority of the monovalent salt were removed between 380 to 410 °C. The treated real produced water was of drinking water quality, with <500 mg/l of total dissolved solid (TDS) and with 100% organics removal. Furthermore, the heat liberated during the organic oxidation could be utilized internally and for electricity generation for enhanced the energy efficiency and lower cost of produced water treatment. With system optimization, the proposed SCWDO process can essentially be made a net zero energy process. A novel process flow diagram for the commercial scale self-powered hybrid SCWDO technology was proposed as a cost-effective produced water treatment to mitigate the environmental crises. Techno-economic analysis showed that produced water treatment cost with SCWDO can be reduced to 2–3 $/m 3 and can be up to 60 % cheaper to traditional deep well reinjection. Additionally, the proposed SCWDO process could achieve net negative CO 2 emission.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Multi-scale study of the deformation mechanisms of thermoelectric p-type half-Heusler Hf 0.44 Zr 0.44 Ti 0.12 CoSb 0.8 Sn 0.2

Increasing the figure of merit ZT of thermoelectric (TE) alloys is a challenge that is currently attempted through various metallurgy methods, including nanostructuring and dislocation engineering. Microstructures with such a level of complexity raise questions about the mechanical reliability of these new materials. Indeed, despite the values of hardness and elastic modulus known for the clear majority of TE materials, the data on deformation mechanisms are still rare. Focusing on the nanostructured p-type half-Heusler Hf 0.44 Zr 0.44 Ti 0.12 CoSb 0.8 Sn 0.2 , our multi-scale study aims to analyze the deformation mechanisms. Experiments conducted at macro-, meso-, and micro-scale are designed to trigger and assess plasticity mechanisms. Compression testing on bulk samples subject to a confining pressure environment and temperature leads to an exclusive brittle failure. The mixed-mode failure mechanisms involve switching between intra- and inter-granular crack propagation, depending on the grain size met by the crack tip. Cube-corner nanoindentation at meso-scale generates cracks and enables fracture toughness estimation, while TEM analysis of the crack tip area confirms no dislocation activity and 3D-Electron Back Scattered Diffraction technique confirms the mixed crack propagation behavior. At micro-scale, micro-pillar compression stress-strain curves and failure mechanisms are comparable with bulk samples testing analysis. These results can be used to provide design guidelines for more crack-resistant TE alloys.

Thermoelectricity↗

DOE OSTI2024

The Scientific Case for Concurrent Neutron and X-ray Scattering and Spectroscopy

The interrogation of materials with X-rays or neutrons to determine the structure, energetics, and dynamics of materials is fundamental to advancing materials' physical and chemical science and developing innovative material technologies. A transcending challenge in developing novel materials is that progress hinges on understanding the structure and dynamics across multiple time and length scales in complex materials that feature multiple components, interfaces, and compositions. Despite the ever-growing demands on materials’ characterization, existing approaches are almost exclusively based on isolated X-ray or neutron scattering, i.e., an approach commensurate with the more narrowly defined needs of fifty years ago. A three-day workshop sponsored by the U.S. National Science Foundation (NSF) analyzed the demand for concurrent neutron and X-ray (NeX) experiments. It was held at the Spring Hill Suites, San Jose, California, from June 2 to 4, 2022. In this workshop, 70 national and international experts ascertained the crucial need to establish NeX capabilities to advance the science of complex materials and systems in the US. Here, we illustrate the need for NeX scattering and spectroscopy experiments by showcasing examples that span areas as diverse as biomaterials, energy science, soft matter, and nanomaterials. To provide NeX capability will require new instrumentation that enables concurrent experiments. Affected areas include chemistry, soft matter, quantum materials, pure and applied chemistry, bioscience, geoscience, and applied materials. NeX benefits research outcomes due to the complementarity of the two techniques, which is essential for better model refinement. While joint refinement of data from separate neutron and X-ray experiments is critical to avoid ambiguities, especially in multiphase-multicomponent materials, concurrent experiments overcome scientific and technical barriers associated with single measurements, separated by location and, thus, time. Among all the examples, these factors introduce uncertainties in the results that complicate data analysis. [1,2] [3] While models are strongly sample-dependent, the principles of joint refinement are generally applicable to these disciplines, including the development of advanced parameterization, modeling, and analysis techniques that also consider the temporal and spatial resolutions of the two methods, leading to unambiguous data interpretation. Solutions for technical barriers must be found to realize NeX experiments, including developing robust sample environments that meet the optical requirements of neutrons and X-rays.

36 MATERIALS SCIENCE↗

NASA NTRS1987

A Lanczos eigenvalue method on a parallel computer

Eigenvalue analyses of complex structures is a computationally intensive task which can benefit significantly from new and impending parallel computers. This study reports on a parallel computer implementation of the Lanczos method for free vibration analysis. The approach used here subdivides the major Lanczos calculation tasks into subtasks and introduces parallelism down to the subtask levels such as matrix decomposition and forward/backward substitution. The method was implemented on a commercial parallel computer and results were obtained for a long flexible space structure. While parallel computing efficiency is problem and computer dependent, the efficiency for the Lanczos method was good for a moderate number of processors for the test problem. The greatest reduction in time was realized for the decomposition of the stiffness matrix, a calculation which took 70 percent of the time in the sequential program and which took 25 percent of the time on eight processors. For a sample calculation of the twenty lowest frequencies of a 486 degree of freedom problem, the total sequential computing time was reduced by almost a factor of ten using 16 processors.

Bostic, Susan W.↗

NASA NTRS1993

A structural and petrographic investigation of the pretoria saltpan impact structure

The Pretoria Saltpan crater is located in the southern portion of the Bushveld Igneous Complex some 40 km NNW of Pretoria, South Africa, at 25 deg 24 min 30 sec S/28 deg 4 min 59 sec E. The near-circular structure of 1.13 km diameter exhibits a well-preserved, uptilted granite rim. Granitic breccia overlies Karroo sediment in places, indicating a post-Karroo age for the cratering event. The coincidence of the spacial occurrence of the crater with respect to various alkaline and ultramafic intrusives has been the main argument put for yard against an impact origin for the structure. Detailed mapping of the crater rim exposures and the crater environs was carried out and revealed many occurrences of intrusives in the whole region. Structural analysis along the rim revealed the presence of typical impact crater related structures. Comparative petrographic and chemical studies of crater-related and non-related intrusives showed close similarities between these sample suites.

Brandt, D.↗

NASA NTRS2000

Mineralogical and Geochemical Analyses of Antarctic Lake Sediments: A Reflectance and Moessbauer Spectroscopy Study with Applications for Remote Sensing on Mars

Lakebottom sediments from the Dry Valleys region of Antarctica have been analyzed here in order to study the influence of water chemistry on the mineralogy and geochemistry of these sediments, as well as to evaluate techniques for remote spectral identification of potential biomarker minerals on Mars. Lakes from the Dry Valleys region of Antarctica have been investigated as possible analogs for extinct lake environments on early Mars. Sediment cores were collected in the present study from perennially ice-covered Lake Hoare in the Taylor Valley. These sediments were taken from a core in an oxic region of the lake and another core in an anoxic zone. Differences between the two cores were observed in the sediment color, Fe(II)/Fe(III) ratio, the presence of pyrite, the abundance of Fe, S and some trace elements, and the C, N and S isotope fractionation patterns. The results of visible-infrared reflectance spectroscopy (0.3-25 microns) Mossbauer spectroscopy (77 and 4 K) and X-ray diffraction are combined to determine the mineralogy and composition of these samples. The sediments are dominated by plagioclase, K-feldspar, quartz and pyroxene. Algal mats grow on the bottom of the lake and organic material has been found throughout the cores. Calcite is abundant in some layers of the aerobic core (shallow region) and pyrite is abundant in some layers of the anaerobic core (deep region). Analysis of the spectroscopic features due to organics and carbonates with respect to the abundance of organic C and carbonate contents was performed in order to select optimal spectral bands for remote identification of these components in planetary regoliths. Carbonate bands near 4 and 6.8 microns (approx.2500 and 1500/cm) were detected for carbonate abundances as low as 0.1 wt.% CO2. Organic features at 3.38, 3.42 and 3.51 microns (2960, 2925 and 2850/cm) were detected for organic C abundances as low as 0.06 wt.% C. The d13C trends show a more complex organic history for the anaerobic sediments than for the aerobic sediments. The biogenic pyrite found in the anaerobic core is associated with lighter d34S values and high organic C levels and could be used as a biomarker mineral for paleolakes on Mars.

Froeschl, Heinz↗

DOE OSTI2023

National User Resource for Biological Accelerator Mass Spectrometry Annual Report

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

National User Resource for Biological Accelerator Mass Spectrometry

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2002

Analysis of Graphite-Reinforced Cementitious Composites

Strategically embedding graphite meshes in a compliant cementitious matrix produces a composite material with relatively high tension and compressive properties as compared to steel-reinforced structures fabricated from a standard concrete mix. Although these composite systems are somewhat similar, the methods used to analyze steel-reinforced composites often fail to characterize the behavior of their more advanced graphite-reinforced counterparts. This Technical Memorandum describes some of the analytical methods being developed to determine the deflections and stresses in graphite-reinforced cementitious composites. It is initially demonstrated that the standard transform section method fails to provide accurate results when the elastic moduli ratio exceeds 20. An alternate approach is formulated by using the rule of mixtures to determine a set of effective material properties for the composite. Tensile tests are conducted on composite samples to verify this approach. When the effective material properties are used to characterize the deflections of composite beams subjected to pure bending, an excellent agreement is obtained. Laminated composite plate theory is investigated as a means for analyzing even more complex composites, consisting of multiple graphite layers oriented in different directions. In this case, composite beams are analyzed using the laminated composite plate theory with material properties established from tensile tests. Then, finite element modeling is used to verify the results. Considering the complexity of the samples, a very good agreement is obtained.

Vaughan, R. E.↗

NASA NTRS2013

Complex Indigenous Organic Matter Embedded in Apollo 17 Volcanic Black Glass Surface Deposits

Papers presented at the first Lunar Science Conference [1] and those published in the subsequent Science Moon Issue [2] reported the C content of Apollo II soils, breccias, and igneous rocks as rang-ing from approx.50 to 250 parts per million (ppm). Later Fegley & Swindle [3] summarized the C content of bulk soils from all the Apollo missions as ranging from 2.5 (Apollo 15) to 280 ppm (Apollo 16) with an overall average of 124+/- 45 ppm. These values are unexpectedly low given that multiple processes should have contributed (and in some cases continue to contribute) to the lunar C inventory. These include exogenous accretion of cometary and asteroidal dust, solar wind implantation, and synthesis of C-bearing species during early lunar volcanism. We estimate the contribution of C from exogenous sources alone is approx.500 ppm, which is approx.4x greater than the reported average. While the assessm ent of indigenous organic matter (OM) in returned lunar samples was one of the primary scientific goals of the Apollo program, extensive analysis of Apollo samples yielded no evidence of any significant indigenous organic species. Furthermore, with such low concentrations of OM reported, the importance of discriminating indigenous OM from terrestrial contamination (e.g., lunar module exhaust, sample processing and handling) became a formidable task. After more than 40 years, with the exception of CH4 [5-7], the presence of indigenous lunar organics still remains a subject of considerable debate. We report for the first time the identification of arguably indigenous OM present within surface deposits of black glass grains collected on the rim of Shorty crater during the Apollo 17 mission by astronauts Eugene Cernan and Harrison Schmitt.

Thomas-Keprta, Kathie L.↗

DOE OSTI2023

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. Here we extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across datasets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS datasets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

59 BASIC BIOLOGICAL SCIENCES↗