Plasmid-encoded gene expression of pathogenic bacteria by antibiotic induction as detected by MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis
Not Available
Fagerquist, Clifton K. (ORCID:0000000225983686)↗
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Results for “HE, ToF, mass spectrometry”
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Curious Case of BiEDOT: MALDI-TOF Mass Spectrometry Reveals Unbalanced Monomer Incorporation with Direct (Hetero)arylation Polymerization
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99 GENERAL AND MISCELLANEOUS↗
Matrix-assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry for Advanced Polymer Charaterization
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Hafenstine, Glenn↗
Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses
Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.
59 BASIC BIOLOGICAL SCIENCES↗
Probing Grain Boundary Segregation in 304L Stainless Steel using Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS).
Abstract not provided.
Ohlhausen, James↗
Extraterrestrial Helium (He@C60) Trapped in Fullerenes in the Sudbury Impact Structure
Fullerenes (C60 and C70) have recently been identified in a shock-produced breccia (Onaping Formation) associated with the 1.85-Ga Sudbury Impact Crater. The presence of parts-per-million levels of fullerenes in this impact structure raises interesting questions about the processes that led to the formation of fullerenes and the potential for delivery of intact organic material to the Earth by a large bolide (e.g., asteroid or comet). Two possible scenarios for the presence of fullerenes in the Sudbury impact deposits are that (1) fullerenes are synthesized within the impact plume from the C contained in the bolide; or (2) fullerenes are already present in the bolide and survived the impact event. The correlation of C and trapped noble gas atoms in meteorites is well established. Primitive meteorites contain several trapped noble gas components that have anomalous isotopic compositions, some of which may have a presolar origin. Several C-bearing phases, including SiC, graphite, and diamond, have been recognized as carriers of trapped noble gases. It has also been suggested that fullerenes (C60 and C70) might be a carrier of noble gas components in carbonaceous chondrites. Recently, fullerenes have been detected in separate samples in the Allende meteorite. Carbon-60 is large enough to enclose the noble gases He, Ne, Ar, Kr, and Xe, but it is too small to contain diatomic gases such as N2 or triatomic gases such as CO2. Recent experimental work has demonstrated that noble gases of a specific isotopic composition can be introduced into synthetic fullerenes at high temperatures and pressures; these encapsulated gases can then be released by the breaking of one or more C bonds during step-heating under vacuum. These thermal-release patterns for He encapsulated within the C60 molecule (He@C60) are similar to the patterns for acid residues of carbonaceous chondrites, suggesting that fullerenes could be an additional carrier of trapped noble gases in acid residues of meteorites. Analysis and Results: In order to characterize the noble gas compositions of the Sudbury fullerenes, we undertook a systematic study of acid-resistant residues throughout the C-rich layer (Black member) of the Onaping Formation. Samples were demineralized and extracted using standard techniques. The Onaping extracts were analyzed using several techniques, including UV-Vis adsorption, electro spray mass spectrometry, and laser desorption (linear and reflectron) time-of-flight (TOF) mass spectrometry (LDMS). The Sudbury fullerenes were then separated and purified using HPLC coupled with a photo diode array detector. The HPLC extracts containing the purified fullerenes were loaded into a metal tube furnace within a glove box under a N atmosphere in preparation for noble gas analyses. The 3-He and 4-He content of the fullerene extracts was measured using previously reported standard techniques . Discussion: Fullerenes (C60 and C70) in the Sudbury Impact Structure have been found to contain trapped He with a 3-He/4-He ratio greater than 5 x 10(exp -4). The 3-He/4-He ratio exceeds the accepted solar value by more than 30% and is more than 10x higher than the maximum reported mantle value. Terrestrial nuclear reactions or cosmic-my bombardment are not sufficient to generate such a high ratio. The 3-He/4-He ratios in the Sudbury fullerenes are similar to those determined for interplanetary dust particles. The greater-than-solar ratios of 3-He/4-He in the Sudbury fullerenes may indicate a presolar origin, although alternative mechanisms occurring in the ISM to explain these high ratios (e.g., spallation reactions, selective He implantation, etc.) cannot be entirely ruled out. We are currently attempting to isolate enough fullerene material to measure anomalous Ne (or Kr or Xe) contained within the C60 (e.g., the "pure" 22-Ne component) and thus determine whether the Sudbury fullerenes are indeed presolar in origin.
Becker, L.↗
TOFHunter—unlocking rapid untargeted screening of inductively coupled plasma–time-of-flight–mass spectrometry data
This study provides an overview of a newly developed open source program written in Python, TOFHunter, which permits the rapid and untargeted screening of inductively coupled plasma (ICP)-time-of-flight (TOF)-mass spectrometry (MS) datasets. ICP-TOF-MS is an analytical tool capable of providing quasi simultaneous detection of all nuclides from Li to Pu. This capability has triggered an increase in studies investigating single-particle analysis in which the TOF-MS provides correlated elemental/isotopic signatures on a particle basis in time. Similarly, laser ablation mapping has seen rapid growth owing to ICP-TOF-MS's capacity to handle fast washout times (<10 ms) while providing a broad nuclide coverage. The caveat to this broad mass coverage and high time resolution comes in the form of large, overwhelming datasets. With datasets typically on the scale of gigabytes, it is easy for a user to only focus on very targeted analytes; however, this focus diminishes the opportunity offered by the TOF-MS detector. TOFHunter applies chemometric methods, principal component analysis (PCA), and interesting features finder (IFF) on ICP-TOF-MS data, allowing for investigation of correlations, major and minor variance sources, and sample screening. The unique spectra identified by the (IFF) are used to generate a list of mass peaks, which are then matched with both nuclides and potential interferences before being exported for the user to investigate. Several case studies are discussed herein, demonstrating TOFHunter's ability to screen aqueous injections, single-particle/single-cell analysis, and probe laser ablation mapping files for unique regions of interest.
47 OTHER INSTRUMENTATION↗
In situ liquid SIMS analysis of uranium oxide
Trace analysis of nuclear materials in solid particles collected in the environment or particles in liquid slurry generated in nuclear material manufacturing processes can pinpoint elemental, organic, and isotopic signatures of nuclear fuel cycle activities and processes. Such information can support nuclear safeguards programs by increasing our ability to detect undeclared nuclear materials, routine activities for safeguarding at declared facilities, and illicit activities. However, trace radioactive material analysis in liquids and slurries is challenging using bulk approaches. For example, one drawback of sensitive analysis such as inductively coupled plasma mass spectrometry (ICP-MS) is that sample is consumed or destroyed as a result of the technical approach. We developed a vacuum compatible microfluidic interface to enable surface analysis of liquids and liquid-solid interactions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). In this work, we illustrate initial results of liquid standards containing uranium using in situ liquid SIMS. Specifically a series of diluted uranium standards used for ICPMS analysis were studied and the limit of detection was estimated. Since the liquid SIMS analysis is almost nondestructive, the same sample can be analyzed by other more destructive approaches afterwards or saved for future references. Consequently, multimodal analysis is possible. Our results demonstrate that in situ liquid SIMS can be used as a new approach to analyze radioactive materials in liquid and slurry forms of relevance to the IAEA safeguards missions.
In situ liquid ToF-SIMS, uranium, limit of detecti↗
Identification of Unknown Contaminants in Water Samples from ISS Employing Liquid Chromatography/Mass Spectrometry/Mass Spectrometry
Mass Spectrometry/Mass Spectrometry (MS/MS) is a powerful technique for identifying unknown organic compounds. For non-volatile or thermally unstable unknowns dissolved in liquids, liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) is often the variety of MS/MS used for the identification. One type of LC/MS/MS that is rapidly becoming popular is time-of-flight (TOF) mass spectrometry. This technique is now in use at the Johnson Space Center for identification of unknown nonvolatile organics in water samples from the space program. An example of the successful identification of one unknown is reviewed in detail in this paper. The advantages of time-of-flight instrumentation are demonstrated through this example as well as the strategy employed in using time-of-flight data to identify unknowns.
Rutz, Jeffrey A.↗
Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water
In September 2010, analysis of ISS potable water samples was undertaken to determine the contaminant(s) responsible for a rise of total organic carbon (TOC) in the Water Processor Assembly (WPA) product water. As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds were initiated, resulting in discovery of an unknown peak in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples and analyzing it by GC/MS in full-scan mode. Although a computer match of the compound identity could not be obtained with the instrument database, a search with a more up-to-date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively coupled plasma/mass spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown compound(s) contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external direct analysis in real time time of flight (DART TOF) mass spectrometry. To routinely test for DMSD in the future, a quantitative method was needed. A preliminary GC/MS method was developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for measuring DMSD.
Rutz, Jeffrey A.↗
Miniature Mass Spectrometers on Space and Planetary Missions
Space flight mass spectrometers contribute our understanding of the origin and evolution of our solar system and even of life itself. This fundamental role has motivated increasing interest in miniature mass spectrometry for planetary missions. Several remarkable new instruments are en route or under development to investigate the composition of planetary bodies such as Mars and comets. For instance, the Sample Analysis at Mars (SAM) suite on the 2009 Mars Science Laboratory (MSL) mission includes a quadrupole mass spectrometer with a sophisticated gas processing system as well as pyrolysis and chemical derivatization protocols for solid samples. Future missions will require even lighter, lower power, and yet more capable mass spectrometers, particularly to analyze samples in situ on planetary surfaces. We have been developing laser-based mass spectrometers for elemental and organic/molecular analysis of rock, ice, or fine particle samples. These typically use time-of-flight (TOF) mass analyzers, which are readily miniaturized and can detect both atomic species and complex organics that occur in a variety of planetary materials. For example, nonvolatile polycyclic aromatic hydrocarbons and kerogen-like macromolecular carbon are found in some carbonaceous meteorites, which derived from asteroid parent bodies. A single focused laser pulse is able to volatilize and ionize some of these compounds for direct TOF analysis. While this is possible without any sample preparation or contact, sensitivity and quantitative performance can improve significantly with some sample handling. As such we have also been examining robotic mechanisms and protocols to accompany space flight mass spectrometers. In addition, sensors in early development may significantly improve these capabilities, via use of techniques such as switchable polarity, ambient pressure, or resonant ionization; tandem mass spectrometry (TOF or ion trap); and chemical imaging.
Brinckerhoff, William↗
Elemental analysis of air-sensitive frozen molten salt samples using an inert transfer chamber for LIBS/LA-ICP-TOF-MS analysis
A novel inert sample transfer system was developed and employed to enable, for the first time, the analysis of air-sensitive salt samples in a two-volume ablation cell using simultaneous laser-induced breakdown spectroscopy (LIBS) and laser ablation (LA)-inductively coupled plasma (ICP)-time-of-flight (TOF)-mass spectrometry (MS) analysis. Molten salts are of growing interest as a medium for advanced nuclear reactors and nuclear fuel reprocessing technologies continue to be developed around their use. However, compositional analysis of molten salt samples can be challenging because of their air-sensitive nature and varying solubilities leading to inaccurate measurements when digested. LA-based analysis provides an alternate method to digestion and can provide rapid elemental information with little sample preparation. In this study, LIBS and LA-ICP-TOF-MS were used to analyze the Ce content in frozen salt samples taken from a series of electrochemical experiments. Calibrations were built for each technique, and the resulting limits of detection for Ce were estimated to be 107 and 58 µg g −1 for LIBS and LA-ICP-TOF-MS, respectively. Test samples from the electrochemical experiments were analyzed using these calibrations. The results matched bulk digestion-based ICP-optical emission spectroscopy values, and daily trends in Ce concentration changes were identified. Additionally, the LIBS and LA-ICP-TOF-MS analysis was demonstrated for identifying microgram per gram levels of components and detecting trace contaminants. The impurities detected by LIBS included Al, Mg, Ca, and Na. The impurities detected by LA-ICP-TOF-MS included W, Ag, Al, Fe, Ni, Mo, Nd, Sm, Th, and U.
Andrews, Hunter B. [Oak Ridge National Laboratory ↗
Product ion distributions using H 3 O + proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS): mechanisms, transmission effects, and instrument-to-instrument variability
Abstract. Proton-transfer-reaction mass spectrometry (PTR-MS) using hydronium ion (H3O+) ionization is widely used for the measurement of volatile organic compounds (VOCs) both indoors and outdoors. H3O+ ionization, as well as the associated chemistry in an ion–molecule reactor, is known to generate product ion distributions (PIDs) that include other product ions besides the proton-transfer product. We present a method, using gas-chromatography pre-separation, for quantifying PIDs from PTR-MS measurements of nearly 100 VOCs of different functional types including alcohols, ketones, aldehydes, acids, aromatics, organohalides, and alkenes. We characterize instrument configuration effects on PIDs and find that reactor reduced electric field strength (E/N), ion optic voltage gradients, and quadrupole settings have the strongest impact on measured PIDs. Through an interlaboratory comparison of PIDs measured from calibration cylinders, we characterized the variability of PID production from the same model of PTR-MS across seven participating laboratories. Product ion variability was generally smaller (e.g., < 20 %) for ions with larger contributions to the PIDs (e.g., > 0.30) but less predictable for product ions formed through O2+ and NO+ reactions. We present a publicly available library of H3O+ PTR-MS PIDs that will be updated periodically with user-provided data for the continued investigation into instrument-to-instrument variability of PIDs.
Link, Michael F. (ORCID:0000000218412455)↗
Enhanced Optical Contrast and Switching in Near‐Infrared Electrochromic Devices by Optimizing Conjugated Polymer Oligo(Ethylene Glycol) Sidechain Content and Gel Electrolyte Composition
Abstract A detailed investigation addressing the effects of functionalizing conjugated polymers with oligo(ethylene glycol) (EG n ) sidechains on the performance and polymer‐electrolyte compatibility of electrochromic devices (ECDs) is reported. The electrochemistry for a series of donor‐acceptor copolymers having near‐infrared (NIR)‐optical absorption, where the donor fragment is 3,4‐ethylenedioxythiophene (EDOT) or an EG n functionalized bithiophene (g2T) and the acceptor fragment is diketopyrrolopyrrole (DPP) functionalized with branched alkyl or EG n sidechains, is extensively probed. ECDs are next fabricated and it is found that EG n sidechain incorporation must be finely balanced to promote polymer‐electrolyte compatibility and provide efficient ion exchange. Proper electrolyte‐cation pairing and polymer structural tuning affords a 2x increase in optical contrast (from 12% to 24%) and >60x reduction in switching time (from 20 to 0.3 s). Atomic force microscopy (AFM)/grazing incidence wide‐angle X‐ray scattering (GIWAXS) characterization of the polymer film morphology/microstructure reveals that an over‐abundance of EG n sidechains generates large polymer crystallites, which can suppress ion exchange. Lastly, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) indicates sidechain/electrolyte identity does not influence the electrolyte penetration depth into the films, and EG n sidechain inclusion increases electrolyte cation uptake. The material structural design insight and guidelines regarding the polymer‐electrolyte ion insertion/expulsion dynamics reported here should be of significant utility for developing next‐generation mixed ionic‐electronic conducting materials.
Chemistry↗
Crossover Effects of Transition‐Metal Ions on Lithium‐Metal Anode in Localized High Concentration Electrolytes
Abstract The stability of the solid–electrolyte interphase (SEI) is critical to the cycle life of lithium‐metal batteries (LMBs). While the crossover effect of transition‐metal ions from cathode to anode is extensively studied in lithium‐ion batteries with graphite anodes, its impact on LMBs remains largely unexplored. Herein, this study investigates the electrochemical and chemical properties of SEI layers formed on lithium‐metal anodes in localized high‐concentration electrolytes (LHCEs) containing dissolved transition‐metal ions (Ni 2+ , Mn 2+ , and Co 2+ ). It is demonstrated that transition‐metal ions in LHCEs reduce the coulombic efficiency (CE) and significantly degrade the cycle life of LMBs. Time‐of‐flight secondary‐ion mass spectrometry (ToF‐SIMS) reveals that SEI structures differ depending on the dissolved TM ion, with Mn 2+ and Co 2+ inducing severe destabilization, and Ni 2+ exhibiting a less severe impact. These findings underscore the detrimental effects of transition‐metal crossover effects in LMB systems.
Guo, Zezhou [Materials Science and Engineering Pro↗
Delineating the Impact of Transition‐Metal Crossover on Solid‐Electrolyte Interphase Formation with Ion Mass Spectrometry
Abstract Lithium‐metal batteries (LMB) employing cobalt‐free layered‐oxide cathodes are a sustainable path forward to achieving high energy densities, but these cathodes exhibit substantial transition‐metal dissolution during high‐voltage cycling. While transition‐metal crossover is recognized to disrupt solid‐electrolyte interphase (SEI) formation on graphite anodes, experimental evidence is necessary to demonstrate this for lithium‐metal anodes. In this work, advanced high‐resolution 3D chemical analysis is conducted with time‐of‐flight secondary‐ion mass spectrometry (TOF‐SIMS) to establish spatial correlations between the transition metals and electrolyte decomposition products found on cycled lithium‐metal anodes. Insights into the localization of various chemistries linked to crucial processes that define LMB performance, such as lithium deposition, SEI growth, and transition‐metal deposition are deduced from a precise elemental and spatial analysis of the SEI. Heterogenous transition‐metal deposition is found to perpetuate both heterogeneous SEI growth and lithium deposition on lithium‐metal anodes. These correlations are confirmed across various lithium‐metal anodes that are cycled with different cobalt‐free cathodes and electrolytes. An advanced electrolyte that is stable to higher voltages is shown to minimize transition‐metal crossover and its effects on lithium‐metal anodes. Overall, these results highlight the importance of maintaining uniform SEI coverage on lithium‐metal anodes, which is disrupted by transition‐metal crossover during operation at high voltages.
Chemistry↗
Revealing the Structural Evolution of Green Rust Synthesized in Ionic Liquids by In Situ Molecular Imaging
Abstract Ionic liquids are green solvents that have wide applications in material synthesis, catalysis, and separation. A model switchable ionic liquid (SWIL) consisting of 1,8‐diazabicycloundec‐7‐ene (DBU) and 1‐hexanol with carbon dioxide (CO 2 ) as the trigger gas is chosen to synthesize nanocrystalline green rust. Under anoxic conditions, by adding iron (II) acetate (Fe(C 2 H 3 O 2 ) 2 ) and methanol to the degassed SWIL, a nanoparticulate green rust with carbonate (nano‐GR) is synthesized. More importantly, the molecular structural change of the ionic liquid resulting in green rust crystallines is first characterized using in situ liquid using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) coupled with the system for analysis at the liquid vacuum interface (SALVI), a vacuum compatible microfluidic reactor in this work. Dimers and ionic clusters consisting ferric and ferrous ions are identified in liquid ToF‐SIMS spectra. Spectral principal component analysis is used to confirm that these ion pairs including dimers and cluster ions are different from nonionic liquids. The results show that liquid ToF‐SIMS can be a useful tool to study complex liquids at the molecular level providing insights into predicative synthesis of nanomaterials using environmentally friendly green solvents and giving unique visualization of the evolving material interface due to nucleation.
Shen, Yanjie↗