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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference—Advancing Biological and Pharmaceutical Mass Spectrometry

Following the highly successful Chinese American Society for Mass Spectrometry (CASMS) conferences in the previous 2 years, the 3rd CASMS Conference was held virtually on August 28–31, 2023, using the Gather. Town platform to bring together scientists in the MS field. The conference offered a 4-day agenda with a scientific program consisting of two plenary lectures, and 14 parallel symposia in which a total of 70 speakers presented technological innovations and their applications in proteomics and biological MS and metabo-lipidomics and pharmaceutical MS. In addition, 16 invited speakers/panelists presented at two research-focused and three career development workshops. Moreover, 86 posters, 12 lightning talks, 3 sponsored workshops, and 11 exhibitions were presented, from which 9 poster awards and 2 lightning talk awards were selected. Furthermore, the conference featured four young investigator awardees to highlight early-career achievements in MS from our society. In conclusion, the conference provided a unique scientific platform for young scientists (i.e. graduate students, postdocs, and junior faculty/investigators) to present their research, meet with prominent scientists, learn about career development, and job opportunities (http://casms.org).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS2023

Evaluation of the Interference of Tenax®TA Adsorbent With Dimethylformamide Dimethyl Acetal Reagent for Gas Chromatography-Dragonfly Mass Spectrometry and Future Gas Chromatography-Mass Spectrometry in Situ Analysis

Among future space missions, national aeronautics and space administration (NASA) selected two of them to analyze the diversity in organic content within Martian and Titan soil samples using a gas chromatograph – mass spectrometer (GC–MS) instrument. The Dragonfly space mission is planned to be launched in 2027 to Titan's surface and explore the Shangri-La surface region for years. One of the main goals of this mission is to understand the past and actual abundant prebiotic chemistry on Titan, which is not well characterized yet. The ExoMars space mission is planned to be launched in 2028 to Mars’ surface and explore the Oxia Planum and Mawrth Vallis region for years. The main objectives focus on the exploration of the subsurface soil samples, potentially richer in organics, that might be relevant for the search of past life traces on Mars where irradiation does not impact the matrices and organics. One recently used sample pre-treatment for gas chromatography – mass spectrometry analysis is planned on both space missions to detect refractory organic molecules of interest for astrobiology. This pre-treatment is called derivatization and uses a chemical reagent – called dimethylformamide dimethyl acetal (DMF-DMA) – to sublimate organic compounds keeping them safe from thermal degradation and conserving the chirality of the molecules extracted from Titan or Mars’ matrices. Indeed, the detection of building blocks of life or enantiomeric excess of some organics (e.g. amino acids) after DMF-DMA pre-treatment and GC–MS analyses would be both bioindicators. The main results highlighted by our work on DMF-DMA and Tenax®TA interaction and efficiency to detect organic compounds at ppb levels in a fast and single preparation are first that Tenax®TA did not show the onset of degradation until after 150 experiments – a 120 h at 300 °C experiment – which greatly exceeds the experimental lifetimes for the DraMS and GC-space in situ investigations. Tenax®TA polymer and DMF-DMA produce many by-products (about 70 and 46, respectively, depending on the activation temperature). Further, the interaction between the two leads to the production of 22 additional by-products from DMF-DMA degradation, but these listed by-products do not prevent the detection of trace-level organic molecules after their efficient derivatization and volatilization by DMF-DMA in the oven ahead the GC–MS trap and column.

DraMS-Dragonfly mission↗
DOE OSTI2024

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗
DOE OSTI2023

2023 American Society for Mass Spectrometry (ASMS) 71st Annual Conference on Mass Spectrometry and Allied Topics

Title (20 words): The investigation of the mechanism for the water splitting by holmium oxide nitrate complex in gas-phase Introduction (120 words): The studies for hydrogen from water splitting is important for clean energy economy as molecular hydrogen is a potential energy carrier. Therefore, understanding the fundamental chemistry of water splitting is essential. The water splitting activated by [Ho(NO3)4]- was previously studied. The suggested mechanism was to first eliminate •NO2 from [Ho(NO3)4]- to make [HoO(NO3)3]-. Then, water was added to form [HoO(NO3)3(H2O)]-, followed by eliminating the •OH to form [HoOH(NO3)3]-. However, we proposed a new mechanism with the formation of [Ho(NO3)3]- prior to the water addition. Once water is added to this intermediate to make [Ho(NO3)3(H2O)]-, the •H is eliminated to form [HoOH(NO3)3]-. Here we have used a labeled experiments with 18-O nitrates. The results to support the new mechanism are discussed.

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

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry

Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich data challenges existing data storage and access technologies, therefore precluding informatics advancements. Here we present MZA™ (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed by a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and efficient programmatic access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

On the importance of color in mass spectrometry imaging

Mass spectrometry imaging (MSI) data visualization relies on heatmaps to show the spatial distribution and measured abundances of molecules within a sample. Non-uniform color gradients such as jet are still commonly used to visualize MSI data, increasing the probability of data misinterpretation and false conclusions. Also, the use of non-uniform color gradients and the combination of hues used in common colormaps makes it challenging for people with color vision deficiencies (CVDs) to visualize and accurately interpret data. Here we present best practices for choosing a colormap to accurately display MSI data, improve readability, and accommodate all CVDs. We also provide other resources on the misuse of color in the scientific field and resources on scientifically derived colormaps presented herein.

47 OTHER INSTRUMENTATION↗
NASA NTRSDate not supplied

Nearest-Neighbor Machine Learning Feature Selection for Interpretation of Microbial Molecular Signatures from Isotope Ratio Mass Spectrometry Data

Mass spectrometry (MS) promises to be a powerful tool for potential biosignature detection during astrobiological missions on ocean worlds in our solar system. Accurate and generalizable machine learning methods could enhance science return on investment by predicting seawater chemistry and classifying isotopic biosignatures, either as a signature consistent with microbial life (biotic) or as a novelty (unclassified/unique). However, machine learning models are likely to be complex and involve interactions between MS features, making biosignatures difficult to interpret. Feature selection methods provide biological and chemical context that help interpret the mechanisms of machine learning models, but these methods also need the ability to detect complex interactions. Previously, we developed a machine learning feature selection algorithm called nearest-neighbor projected distance regression (NPDR) that has the ability to identify important model features that involve complex interactions and automatically reduce correlation and the dimensionality in a high-dimensional variable space. The standard distance metrics used in NPDR – Manhattan and Euclidean – assume the multivariate data are isotropic, which is often violated in real data due to differences in the covariance between variables. Thus, we extend NPDR to include a random forest distance, and other anisotropic distance metrics, for computing nearest neighbors. We also augment the isotope-ratio MS data with time-series features from the raw MS signal to improve biotic classification. We test NPDR on our novel experimental ocean world seawater analog MS data. We measure isotope fractionations of volatile CO 2 that could be measured in exospheres or plumes. Samples include baseline abiotic conditions using a range of possible seawater chemistry consistent with Europa and Enceladus, and biotic samples that include microbes in these seawaters. We use penalized NPDR with random forest proximity to identify interpretable microbial molecular signatures. We compare features with random forest importance, and we train a classifier that discriminates between biotic and abiotic samples with high accuracy. These ML-trained ocean-world analog MS data could be used to assist in identifying biosignatures during future missions.

geochemistry↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2025

Advancing Aerosol Chemical Characterization and Vertical Profiling over the Southern Great Plains Using Uncrewed Aerial Sampling and Offline Aerosol Mass Spectrometry

Recent advancements in uncrewed aerial systems (UASs) and particulate matter (PM) analytical techniques have provided opportunities for atmospheric research. In this study, we deployed the Department of Energy’s fixed-wing ArcticShark UAS to examine PM 2.5 composition at varying altitudes─within and above the planetary boundary layer (PBL)─over the Southern Great Plains atmospheric observatory (SGP). A total of 22 flights were conducted across March, June, and August 2023. Composite filter samples were collected during each flight and analyzed with offline aerosol mass spectrometry (AMS), complemented by on-board real-time sensors and ground-based instrumentation, to provide a comprehensive view of regional aerosol characteristics. Results show clear vertical and seasonal differences in the aerosol composition. Relative to ground-level measurements, aloft samples exhibited shifts in the distribution of organic and inorganic PM, with the organic composition varying distinctly across seasons. Particulate organic nitrogen (ON) was elevated, with bulk compositions similar in March and June but strongly altered in August, likely driven by biomass burning and enhanced photochemical activity. Combined AMS and chemical ionization mass spectrometry analyses detected amines, amides, and amino acids. PM above the planetary boundary layer was enriched in oxidized organic aerosols, while ground-level PM contained higher nitrate and sulfate. Seasonal differences in aqueous-phase processing were also observed, which were strongest in March during persistent cloud cover and weaker in the drier August period, suggesting a shift from aqueous- to gas-phase SOA formation. In conclusion, these findings highlight the value of UAS in advancing PM measurements and vertical profiling of aerosol composition.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1978

Mass spectrometry

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

Burlingame, A. L.↗
NASA NTRS1966

Mass Spectrometry.

Book on mass spectrometry principles and application to ion and neutral atom composition of upper atmosphere

IONOSPHERIC COMPOSITION↗
DOE OSTI2023

A review on recent machine learning applications for imaging mass spectrometry studies

Imaging mass spectrometry (IMS) is a powerful analytical technique widely used in biology, chemistry, and materials science fields that continue to expand. IMS provides a qualitative compositional analysis and spatial mapping with high chemical specificity. The spatial mapping information can be 2D or 3D depending on the analysis technique employed. Due to the combination of complex mass spectra coupled with spatial information, large high-dimensional datasets (hyperspectral) are often produced. Therefore, the use of automated computational methods for an exploratory analysis is highly beneficial. The fast-paced development of artificial intelligence (AI) and machine learning (ML) tools has received significant attention in recent years. These tools, in principle, can enable the unification of data collection and analysis into a single pipeline to make sampling and analysis decisions on the go. There are various ML approaches that have been applied to IMS data over the last decade. Here, in this review, we discuss recent examples of the common unsupervised (principal component analysis, non-negative matrix factorization, k-means clustering, uniform manifold approximation and projection), supervised (random forest, logistic regression, XGboost, support vector machine), and other methods applied to various IMS datasets in the past five years. The information from this review will be useful for specialists from both IMS and ML fields since it summarizes current and representative studies of computational ML-based exploratory methods for IMS.

47 OTHER INSTRUMENTATION↗
NASA NTRS1972

Mass spectrometry.

Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

Burlingame, A. L.↗
NASA NTRS1972

Spacecraft applications of quadrupole mass spectrometry

Techniques of mass spectrometry are reviewed and the theory of the quadrupole mass spectrometer (QMS) is discussed. The QMS is shown to have several advantages over older types of mass spectrometers. The QMS has been flown on a large number of rockets and several satellites. More sophisticated versions of the QMS are proposed for future satellites. Special emphasis is placed on problems of contamination which are likely to be encountered on a large and complex satellite like the Advanced Technology Satellite ATS-G. The development of a QMS to detect and forestall such contamination is discussed.

Thekaekara, M. P.↗