SEARCH · Engineering Papers
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Mass spectrometry and gas chromatography in analysis of organic compounds present in extraterrestrial bodies to provide information on existence of life
Identifying the short-lived intermediates and reaction mechanisms of multi-channel radical cation fragmentation processes remains a current and important challenge to understanding and predicting mass spectra. We find that coherent oscillations in the femtosecond time-dependent yields of several product ions following ultrafast strong-field ionization represent spectroscopic signatures that elucidate their mechanism of formation and identify the intermediate(s) they originate from. Experiments on endo-dicyclopentadiene show that vibrational frequencies from various intermediates are mapped onto their resulting products. Aided by ab initio methods, we identify the vibrational modes of both the cleaved and intact molecular ion intermediates. These results confirm stepwise and concerted fragmentation pathways of the dicyclopentadiene ion. This study highlights the power of tracking the femtosecond dynamics of all product ions simultaneously and sheds further light onto one of the fundamental reaction mechanisms in mass spectrometry, the retro-Diels Alder reaction.
Introduction: In 2019, the National Aeronautics and Space Administration (NASA) announced that it would seek to have humans return to the moon by 2024 in the hopes of establishing a more sustainable lunar presence by 2028. This goal comes with many challenges, one of upmost importance will be to utilize resources that can be found on the moon. Water, which has been identified in the lunar Polar Regions, will be a key resource for in-situ resource utilization (ISRU), as it is capable of being processed for vehicular fuel, as well as life support systems materials such as oxygen. Upcoming Commercial Lunar Payload Services (CLPS) missions will be critical for these resource assessments. Methods: A modified commercial off-the-shelf (COTS) mass spectrometer developed at Kennedy Space Center known as MSolo, consisting of a quadrupole mass filter and space rated electronics undergoes testing and modifications in order to study operational parameters to unconventional approaches needed in flight situations. In general, MSolo operates in the 0-100 m/z range with the ability to detect with a faraday cup (FC) or an electron multiplier (EM) for enhanced detection. A crossbeam (XB) ionization source is used. Preliminary Data: Prior to construction, little information was available on how the MSolo system would perform at lunar like environments, factors such as temperatures (possible fluctuations from 70 to -45 °C), vibrations from launch and their side effects, the general ability to operate while the entire system (hardware and electronic components) were in a vacuum environment, were factors that while know to flight instruments, were something new to a modified COTS system. As components start to warm up, temperature becomes a key factor (ie. heat can no longer escape the electronics as no atmosphere is present), therefore it becomes crucial to find new ways to maintain stable signals and keep the instrument tuned. Calibration itself becomes an important parameter that needs to be performed while maintaining all flight like characteristics. Even the structure itself of MSolo’s sensor needed to be changed to survive the verification parameters needed to be approved for flight. Most important, all the modifications made to the COTS system have to keep the instrument working at the same specifications of the standard commercial systems. Novel Aspect: Results gathered provide key parameters that will assist to the unconventional mass spectrometry approaches of the upcoming CLPS missions to which MSolo has been selected to.
Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.
Advances in multi-collector inductively coupled plasma-mass spectrometry (MC-ICP-MS) have led to the widespread use of iron (Fe) isotopes to elucidate the (bio)geochemical history of a range of environments. To generate Fe isotope ratio measurements, standard-sample bracketing (SSB) is commonly used to correct for instrumental mass bias inherent to MC-ICP-MS. However, SSB is only accurate when sample and isotope standard Fe concentrations match, in addition to the bulk solution matrix. When the Fe concentrations differ, Fe isotope ratio measurement results may be inaccurate, a phenomenon known as the "self-induced matrix effect." Here, this study systematically characterised the self-induced matrix effect for dry plasma Fe isotope ratio measurements on three MC-ICP-MS instruments and three introduction systems. Our extensive dataset indicates that: (1) the degree of mass bias is consistent regardless of MC-ICP-MS front-end design, (2) the degree of mass bias becomes less reproducible as the concentration difference between the sample and bracketing standard increases, and (3) this applies to both pure Fe solutions and solutions from geological materials. This study reinforces the requirement to match bracketing standard and sample concentrations within 10% and provides a correction method for that fall beyond the recommended concentration range to subsequently allow for proper concentration matching during SSB.
Analysis of irradiated material shortly after irradiation can be non-trivial due to highly radioactive activation and fission isotopes increasing dead time in gamma-ray detection systems, often requiring a “cooling-period” between receipt of a sample and the subsequent analysis. A direct separation–detection method has been developed combining ion chromatography and inductively coupled mass spectrometry for rapid, low-level analysis of fission products; it cannot, however, detect certain short-lived species below the detection limit of the system. In this paper we report the implementation of an inline gamma-ray detector, which was added post-separation, pre-analysis, to test the quality and utility of elementally-isolated gamma-ray spectroscopy.
Chemical analysis of sediment and oil hydrocarbon content by gas chromatography and mass spectrometry to establish inception period of bio-organic evolution
Mass spectrometry capabilities of cold cathode magnetron ion source for use in ultrahigh vacuum residual gas analysis
Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.
Calcium is important for the growth and development of plants. It serves crucial functions in cell wall and cell membrane structure and serves as a secondary messenger in signaling pathways relevant to nutrient and immunity responses. Thus, measuring calcium levels in plants is important for studies of plant biology and for technology development in food, agriculture, energy, and forest industries. Often, calcium in plants has been measured through techniques such as atomic absorption spectrophotometry (AAS), inductively coupled plasma–mass spectrometry (ICP-MS), and electrophysiology. These techniques, however, require large sample sizes, chemical extraction of samples or have limited spatial resolution. Here, we used near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the calcium L- and K-edges to measure the calcium to carbon mass ratio with spatial resolution in plant samples without requiring chemical extraction or large sample sizes. We demonstrate that the integrated absorbance at the calcium L-edge and the edge jump in the fluorescence yield at the calcium K-edge can be used to quantify the calcium content as the calcium mass fraction, and validate this approach with onion epidermal peels and ICP-MS. We also used NEXAFS to estimate the calcium mass ratio in hypocotyls of a model plant, Arabidopsis thaliana , which has a cell wall composition that is similar to that of onion epidermal peels. These results show that NEXAFS spectroscopy performed at the calcium edge provides an approach to quantify calcium levels within plants, which is crucial for understanding plant physiology and advancing plant-based materials.
Plants are important sources of energy and materials, and they collectively represent a critical component of Earth’s ecosystem. With increasing environmental stresses due to climate change and intensive agricultural practices, the need for resilient plants is greater than ever before. To secure plant resources for bioenergy, biomaterials, food, and ecosystem adaptation, a deeper understanding of the fundamental biology of plants at a cellular level is urgently needed. Plants contain a multitude of specialized cell types that compose tissues and organs. Pathogens often target specific cell types within plants, and the response of one cell to a particular stimulus is likely to be distinct from its neighbor because of underlying molecular and contextual differences. Understanding how these responses are distributed among cells, the main goal of single-cell approaches, will substantially enhance our ability to use targeted engineering for improving plant productivity and resilience. Furthermore, single-cell approaches are necessary to understand the interactions between plants and other ecosystem members such as fungi, bacteria, and archaea. Unlocking these gene-response mechanisms at a cellular level can improve our ability to adapt plants to environmental stresses, increasing their utility as feedstocks for biomaterials and bioenergy. Recent advances in high-throughput sequencing, mass spectrometry, microfluidics and miniaturization, artificial intelligence and machine learning, and bioinformatics have greatly improved our ability to detect and understand processes at a cellular level. In mammalian systems, single-cell transcriptomics has already led to many advances, such as newly identified cell types and cell-targeted treatment of diseases, and mass spectrometry-based single-cell proteomics has recently been demonstrated as a promising emerging technology. However, plant single-cell omics has lagged behind mammalian approaches due to the high cost of the technologies relative to available resources and to the innate biological features of plants, including the complexity of the cell wall and polyploidy. To better understand how single-cell methods could enable plant science, Lawrence Berkeley National Laboratory (Berkeley Lab) hosted a workshop on April 29, 2021, that brought together a diverse group of leaders in plant and/or single-cell biology. Attendees represented federal research programs and domestic and international academic institutions. During the workshop, three presenters described the current state of research in both experimental and computational approaches. While the focus of the workshop was on factors preventing plant biology researchers from fully adopting single-cell methodologies, workshop participants agreed that most barriers could be overcome with focused, strategic investment and coordinated efforts among institutions leading to significant scientific discoveries that would be difficult to obtain using more conventional technologies.
Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low abundance proteins. Herein, we describe an ion mobility-enhanced mass spectrometry acquisition and peptide identification method, TIFF (Transferring Identification based on FAIMS Filtering), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes.
The fate of organic matter in carbonaceous meteorites during hypervelocity (1-2 km/sec) impacts is investigated using results of experiments in which three samples of the Murchison (CM2) carbonaceous chondrite were shocked to 19, 20, and 36 GPa and analyzed by highly sensitive thermal-desorption photoionization mass spectrometry (SALI). The thermal-desorptive SALI mass spectra of unshocked CM2 material revealed presence of indigenous aliphatic, aromatic, sulfur, and organosulfur compounds, and samples shocked to about 20 GPa showed little or no loss of organic matter. On the other hand, samples shocked to 36 GPa exhibited about 70 percent loss of organic material and a lower alkene/alkane ratio than did the starting material. The results suggest that it is unlikely that the indigenous organic matter in carbonaceous chondritelike planetesimals could have survived the impact on the earth in the later stages of earth's accretion.
The reaction between a sputtered-deposited Ta film (320 nm thick) and a single crystalline (001) beta-SiC substrate induced by vacuum annealing at temperatures of 600-1200 C for 1 h (30 min at 1100 C) is investigated by 3 MeV He(+2) backscattering spectrometry, x-ray diffraction, secondary ion mass spectrometry, and transmission and scanning electron microscopies. No significant reaction is observed at 800 C or at lower tempertures. At 900 C, the main product phases are Ta2C and carbon-stabilized Ta5Si3. A minor amount of unreacted Ta is also present. After annealing at 1000 C, all the tantalum has reacted; the reaction zone possesses a multilayered structure of beta-SiC/TaC/carbon-stabilized Ta5Si3/alpha-Ta5Si3/Ta2C. The diffusion path at 1000 C is plotted on the isothermal section of the Ta-Si-C phase diagram. At 1100 C, the reacted layer has an interface with the SiC substrate that is still quite flat but has a rough surface due to the formation of macroscopic voids within the reacted layer. The equilibrium products predicted by the phase diagram are TaC and TaSi2. This final state is reached by annealing at 1200 C for 1 h. At that point, the reacted layer has a latterally very uneven structure and morphology.
Asteroid 4 Vesta is quite likely the parent asteroid of the howardite, eucrite and diogenite meteorites - the HED clan. Eucrites and diogenites are the products of igneous processes; the former are basaltic composition rocks from flows, and shallow and deep intrusive bodies, whilst the latter are cumulate orthopyroxenites thought to have formed deep in the crust. Impact processes have excavated these materials and mixed them into a suite of polymict breccias. Howardites are polymict breccias composed mostly of clasts and mineral fragments of eucritic and diogenitic parentage, with neither end-member comprising more than 90% of the rock. Early work interpreted howardites as representing the lithified regolith of their parent asteroid. Recently, howardites have been divided into two subtypes; fragmental howardites, being a type of non-regolithic polymict breccia, and regolithic howardites, being lithified remnants of the active regolith of 4 Vesta. We are in the thralls of a collaborative investigation of the record of impact mixing contained within howardites, which includes studies of their mineralogy, petrology, bulk rock compositions, and bulk rock and clast noble gas contents. One goal of our investigation is to test the hypothesis that some howardites represent breccias formed from an ancient, well-mixed regolith on Vesta. Another is to use our results to further understand regolith processing on differentiated asteroids as compared to what has been learned from the Moon. We have made petrographic observations and electron microprobe analyses on 21 howardites and 3 polymict eucrites. We have done bulk rock analyses using X-ray fluorescence spectrometry and are completing inductively coupled plasma mass spectrometry analyses. Here, we discuss our petrologic and bulk compositional results in the context of regolith formation. Companion presentations describe the noble gas results and compositional studies of low-Ca pyroxene clasts.
Cryogenic superconducting tunnel junction (STJ) detectors have the advantage of single-particle sensitivity, high quantum efficiency, low noise, and the ability to detect the time and relative impact energy of deposited ions. This makes them attractive for use in mass spectrometry (MS) and as a form of energy spectrometry. STJ cryodetectors have been coupled to time-offlight (TOF) mass spectrometers equipped with a matrix-assisted laser desorption ionization (MALDI) source and to an electrospray ionization (ESI) TOF mass spectrometer. Here, a lab-made linear ion trap (LIT) mass spectrometer system was coupled to an ESI source and a 16-channel Nb-STJ array with improved readout electronics. The goal was to investigate fundamentals of ESI-generated protein ions by further exploiting the advantage of resolving these ions in a third dimension of the relative energy deposited into the STJs. The proteins equine cytochrome c, bovine carbonic anhydrase, bovine serum albumin, and murine immunoglobulin G were studied using this ESI-LIT-STJ-MS instrument. Multiply charged monomers, multimers, and fragments from metastable ions were resolved from monomer peaks by differences in ion deposition energy even when these ions have the same mass-to-charge ratio as the corresponding monomer. The determination of fragment mass from metastable decomposition is accomplished without knowing the charge state of the fragment. The average charge state of the multimers is reduced with each addition of a protein which is a direct reflection of the surface area available for charging. Multiply charged in-source fragments have also been observed and distinguished in the mass spectrum of carbonic anhydrase by using the differences in the energy deposited in the STJs.
Abstract Background Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. Results This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn 2+ -peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn 2+ -peroxidase. Gas chromatography–mass spectrometry (GC–MS) and two-dimensional 1 H– 13 C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C–C bond ( β-β , β -5, and β -1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C–O bond ( β -O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. Conclusions Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion. Graphical Abstract
Future missions to Enceladus, Europa, Mars, and beyond may seek the molecular signs of extraterrestrial life through chemical analysis of acquired samples. Particularly on ocean worlds such as Enceladus and Europa, samples may contain trace ocean-borne molecular biosignatures of extant life that may or may not share similarities to those of terrestrial life. In situ analyses must be prepared to detect and characterize a wide range of possible molecular species, structures, and patterns, typically with exquisite sensitivity and within a complex, poorly-characterized planetary environment. The Extraterrestrial Molecular Indicators of Life Investigation (EMILI) is designed to meet or exceed the requirements of such missions for organic molecular analysis through a powerful combination of dual chemical separation and both optical and mass spectrometry detection techniques, realized in an integrated, compact instrument package fully compatible with anticipated flight resources and conditions. The full EMILI instrument combines two sample analysis subsystems to provide wide-ranging and complementary detection of organic compounds and inorganic salts. The Gas Analysis Processing System (GAPS) uses a chemical derivatization protocol with gas chromatography (GC) separation prior to detection in an ion trap mass spectrometer (ITMS) to enable full characterization of lower-polarity, volatile and semi-volatile molecules such as fatty acids and hydrocarbons. The Organic Capillary Electrophoresis ANalysis System (OCEANS) uses a liquid-based extraction protocol with CE separation to enable precise analysis of more water-soluble/polar compounds. OCEANS features a laser-induced fluorescence detection mode to perform ultra-sensitive quantitative analysis of chiral amino acids. In EMILI, OCEANS is additionally coupled to the same ITMS through a novel electrospray ionization interface. The common ITMS allows EMILI to identify and cross-correlate molecular species and patterns, detected through either or both protocols, of molecular weights to over 1000 u, potentially even revealing complex biosignatures such as alien oligopeptides and informational polymers.