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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

LipidMiner: A Software for Automated Identification and Quantification of Lipids from Multiple Liquid Chromatography-Mass Spectrometry Data Files

We have developed a tool for automated, high-throughput analysis of LC-MS/MS data files, which greatly simplifies LC-MS based lipidomics analysis. Our results showed that LipidMiner is accurate and comprehensive in identification and quantification of lipid molecular species. In addition, the workflow implemented in LipidMiner is not limited to identification and quantification of lipids. If a suitable metabolite library is implemented in the library matching module, LipidMiner could be reconfigured as a tool for general metabolomics data analysis. It is of note that LipidMiner currently is limited to singly charged ions, although it is adequate for the purpose of lipidomics since lipids are rarely multiply charged,[14] even for the polyphosphoinositides. LipidMiner also only processes file formats generated from mass spectrometers from Thermo, i.e. the .RAW format. In the future, we are planning to accommodate file formats generated by mass spectrometers from other predominant instrument vendors to make this tool more universal.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Comparative Evaluation of Preprocessing Freeware on Chromatography/Mass Spectrometry Data for Signature Discovery

Preprocessing software is crucial for the discovery of chemical signatures in metabolomics, chemical forensics, and other signature-focused disciplines that involve analyzing large data sets from chemical instruments. Here, four freely available and published preprocessing tools known as metAlign, MZmine, SpectConnect, and XCMS were evaluated for impurity profiling using nominal mass GC/MS data and accurate mass LC/MS data. Both data sets were previously collected from the analysis of replicate samples from multiple stocks of a nerve-agent precursor. Each of the four tools had their parameters set for the untargeted detection of chromatographic peaks from impurities present in the stocks. The peak table generated by each preprocessing tool was analyzed to determine the number of impurity components detected in all replicate samples per stock. A cumulative set of impurity components was then generated using all available peak tables and used as a reference to calculate the percent of component detections for each tool, in which 100% indicated the detection of every component. For the nominal mass GC/MS data, metAlign performed the best followed by MZmine, SpectConnect, and XCMS with detection percentages of 83, 60, 47, and 42%, respectively. For the accurate mass LC/MS data, the order was metAlign, XCMS, and MZmine with detection percentages of 80, 45, and 35%, respectively. SpectConnect did not function for the accurate mass LC/MS data. Larger detection percentages were obtained by combining the top performer with at least one of the other tools such as 96% by combining metAlign with MZmine for the GC/MS data and 93% by combining metAlign with XCMS for the LC/MS data. In terms of quantitative performance, the reported peak intensities had average absolute biases of 41, 4.4, 1.3 and 1.3% for SpectConnect, metAlign, XCMS, and MZmine, respectively, for the GC/MS data. For the LC/MS data, the average absolute biases were 22, 4.5, and 3.1% for metAlign, MZmine, and XCMS, respectively. In summary, metAlign performed the best in terms of peak discovery; however, more than one preprocessing tool should be considered to avoid missing potential chemical signatures.

chemical forensics, chemometrics↗
DOE OSTI2024

Exploring Ion Mobility Mass Spectrometry Data File Conversions to Leverage Existing Tools and Enable New Workflows

Ion mobility (IM) is often combined with LC-MS experiments to provide an additional dimension of separation for complex sample analysis. While highly complex samples are better characterized by the full dimensionality of LC-IM-MS experiments to uncover new information, downstream data analysis workflows are often not equipped to properly mine the additional IM dimension. For many samples the data acquisition benefits of including IM separations are all that is necessary to uncover sample information and the full dimensionality of the data is not required for data analysis. Post-acquisition reduction and adaptation of the dimensions of LC-IM-MS and IM-MS experiments into an LC-MS format opens the possibility to use a plethora of existing software tools. In this work, we developed data file conversion tools to reduce the complexity of IM data analysis. Three data file transformations are introduced in the PNNL PreProcessor software: 1) mapping the IM axis to the LC axis for IM-MS data, 2) converting the drift time vs. m/z space to CCS/z vs m/z space, and 3) transforming All Ions IM/MS mobility aligned fragmentation data to a standard LC-MS DDA data file format. Finally, these new data file conversions are demonstrated with corresponding lipidomics and proteomics workflows that leverage existing LC-MS data analysis software to highlight the benefits of the data transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Author Correction: A universal language for finding mass spectrometry data patterns

Correction to: Nature Methodshttps://doi.org/10.1038/s41592-025-02660-z, published online 12 May 2025. This article was originally published under standard Springer Nature license (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license, © The Author(s). The error has been corrected in the HTML and PDF versions of the article.

Damiani, Tito↗
NASA NTRS1988

Image processing software for imaging spectrometry data analysis

Imaging spectrometers simultaneously collect image data in hundreds of spectral channels, from the near-UV to the IR, and can thereby provide direct surface materials identification by means resembling laboratory reflectance spectroscopy. Attention is presently given to a software system, the Spectral Analysis Manager (SPAM) for the analysis of imaging spectrometer data. SPAM requires only modest computational resources and is composed of one main routine and a set of subroutine libraries. Additions and modifications are relatively easy, and special-purpose algorithms have been incorporated that are tailored to geological applications.

Mazer, Alan↗
NASA NTRS1989

Inversion of imaging spectrometry data using singular value decomposition

The use of imaging spectrometers, which acquire data that are both spectrally contiguous images and spatially contiguous spectra, for quantitative remote sensing of the earth is addressed. Such data sets cannot be analyzed fully using either existing spectroscopic or image techniques. Singular value decomposition (SVD) is used here for spectral unmixing and determination of the spatial scales of mixing. It is shown that when it is used to invert the mixing endmember library, SVD allows more insight into library characteristics and more control of the inversion process than other commonly used matrix inversion techniques.

Boardman, Joe W.↗
NASA NTRS1995

Calibration to surface reflectance of terrestrial imaging spectrometry data: Comparison of methods

Many algorithms for spectral analysis of imaging spectroscopy data of the Earth's surface require that the data be calibrated to surface reflectance. Calibration requires removing instrumental response, solar irradiance, atmospheric transmittance, and atmospheric scattering from the radiance detected at the sensor. Depending on the amount of support data, this can be a formidable task. This paper examines four methods of calibration: (1) a radiative transfer model from the University of Colorado (ATREM: Gao and Goetz, 1990; Gao et al., 1992), (2) a MODTRAN-based method developed at the Jet Propulsion Lab by Green et al., (1191), (3) a ground calibration using known sites as standards, and (4) a combined approach using radiative transfer methods and ground calibration. Data from the Airborne Visual and Infra-Red Imaging Spectrometer (AVIRIS) instrument were evaluated from data sets obtained over multiple years and multiple sites.

Clark, Roger N.↗
NASA NTRS1995

High Accuracy In-Flight Wavelength Calibration of Imaging Spectrometry Data

Accurate wavelength calibration of imaging spectrometer data is essential if proper atmospheric transmission corrections are to be made to obtain apparent surface reflectance. Accuracies of 0.1 nm are necessary for a 10 nm-sampling instrument in order to match the slopes of the deep atmospheric water vapor features that dominate the 0.7-2.3 micrometer regions. The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) is calibrated in the laboratory to determine the wavelength position and full-width-half-maximum (FWHM) response for each of the 224 channels. The accuracies are limited by the quality of the monochromator used as a source. The accuracies vary from plus or minus to plus or minus 1.5 nm depending on the wavelength region, in general decreasing with increasing wavelength. Green et al. make corrections to the wavelength calibrations by using the known positions of 14 atmospheric absorption features throughout the 0.4-2.5 micrometer wavelength region. These features, having varying width and intensity, were matched to the MODTRAN model with a non-linear least squares fitting algorithm. A complete calibration was developed for all 224 channels by interpolation. Instrument calibration cannot be assumed to be stable to 0.1 nm over a flight season given the rigors of thermal cycling and launch and landing loads. The upcoming sensor HYDICE will require a means for in-flight spectral calibration of each scene because the calibration is both temperature and pressure sensitive. In addition, any sensor using a two-dimensional array has the potential for systematic wavelength shifts as a function of cross-track position, commonly called 'smile'. Therefore, a rapid means for calibrating complete images will be required. The following describes a method for determining instrument wavelength calibration using atmospheric absorption features that is efficient enough to be used for entire images on workstations. This study shows the effect of the surface reflectance on the calibration accuracy and the calibration history for the AVIRIS B spectrometer over the 1992 flight season.

Goetz, Alexander F. H.↗
DOE OSTI2018

High-Resolution Gamma Spectrometry Data Set for High Burnup Pressurized Water Reactor Used Fuel

Over the past decade, considerable resources have been applied to investigate verification of used nuclear fuel assemblies for international safeguards. The opportunity to expand the available data used to validate these verification techniques was presented in 2016 by the High Burnup Spent Fuel Data Project, which made 25 high-burnup pressurized water reactor used fuel rods available for measurement in the Irradiated Fuels Examination Laboratory at Oak Ridge National Laboratory. With the support of the National Nuclear Security Administration Office of Nonproliferation and Arms Control, a 2017 campaign measured the 25 used fuel rods with a high-resolution gamma spectrometer. A planar high-purity germanium detector was used to provide high-efficiency across an energy range from 60 keV to 3 MeV. Gamma spectra of individual fuel rods were collected in 4.5 mm steps along the entire length of each rod. In addition, spectra were collected on select rods in rotational increments of 30 degrees to provide data on the distribution of fission products along the rod perimeter. The spectra are stored on a controlled-access website for use by others. This paper describes the measurement geometry, used fuel rod characteristics, example spectra, and preliminary analyses performed during the measurement campaign.

Smith, Susan↗
DOE OSTI2018

Evaluation of Digital Image Recognition Methods for Mass Spectrometry Imaging Data Analysis

Analyzing mass spectrometry imaging data can be laborious and time consuming, and as the size and complexity of datasets grow, so does the need for robust automated processing methods. We here present a method for comprehensive, semi-targeted discovery of molecular distributions of interest from mass spectrometry imaging data, using widely available image similarity scoring algorithms to rank images by spatial correlation. A fast and powerful batch search method using a MATLAB implementation of structural similarity (SSIM) index scoring with a pre-selected reference distribution is demonstrated for two sample imaging datasets, a plant metabolite study using Artemisia annua leaf, and a drug distribution study using maraviroc-dosed macaque tissue. .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

BASTet: Shareable and Reproducible Analysis and Visualization of Mass Spectrometry Imaging Data via OpenMSI

Mass spectrometry imaging (MSI) is a transformative imaging method that supports the untargeted, quantitative measurement of the chemical composition and spatial heterogeneity of complex samples with broad applications in life sciences, bioenergy, and health. While MSI data can be routinely collected, its broad application is currently limited by the lack of easily accessible analysis methods that can process data of the size, volume, diversity, and complexity generated by MSI experiments. The development and application of cutting-edge analytical methods is a core driver in MSI research for new scientific discoveries, medical diagnostics, and commercial-innovation. However, the lack of means to share, apply, and reproduce analyses hinders the broad application, validation, and use of novel MSI analysis methods. To address this central challenge, we introduce the Berkeley Analysis and Storage Toolkit (BASTet), a novel framework for shareable and reproducible data analysis that supports standardized data and analysis interfaces, integrated data storage, data provenance, workflow management, and a broad set of integrated tools. Based on BASTet, we describe the extension of the OpenMSI mass spectrometry imaging science gateway to enable web-based sharing, reuse, analysis, and visualization of data analyses and derived data products. Here, we demonstrate the application of BASTet and OpenMSI in practice to identify and compare characteristic substructures in the mouse brain based on their chemical composition measured via MSI.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometry data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗