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At least 757 records · Page 42

ToF-SIMS spectral data analysis of Paenibacillus sp. 300A biofilms and planktonic cells

Analysis of bacterial biofilms is particularly challenging and important with diverse applications from systems biology to biotechnology. Among the variety of techniques that have been applied, time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many promising features in studying the surface characteristics of biofilms. ToF-SIMS offers high spatial resolution and high mass accuracy, which permit surface sensitive analysis of biofilm components. Thus, ToF-SIMS provides a powerful solution to addressing the challenge of bacterial biofilm analysis. This dataset covers ToF-SIMS analysis of Paenibacillus sp. 300A (300A) isolated from the Hanford site in Richland, WA. The strain is known to have metal and sulfur reducing properties and can be used for bioremediation, wastewater treatment, bioengineering and technology development. There is a current need to identify small molecules and fragments produced from bacterial biofilms. Static ToF-SIMS spectra of 300A were obtained using an IONTOF TOF-SIMS V instrument equipped with a 25 keV Bi 3 + metal ion gun. Identified molecules and molecular fragments are compared against known biological databases and the reported peaks have at least 65 ppm mass accuracy. These molecules range from lipids and fatty acids to flavonoids, quinolones, and other naturally occurring organic compounds. It is anticipated that the spectral identification of key peaks will assist detection of metabolites, extracellular polymeric substance molecules like polysaccharides, and biologically relevant small molecules using ToF-SIMS in future surface and interface research of bacterial biofilms.

Biofilms↗

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics and exposomics studies is to fully characterize the small molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversi-ty present within the metabolome and exposome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemis-try methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alter-native route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solu-tion. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectros-copy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics and exposomics studies. We expect this review will inspire researchers in the field of small molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Metabolism↗

Plasma proteomic biomarkers of physical frailty in heart failure: a propensity score matched discovery-based pilot study

Background: Physical frailty is highly prevalent in heart failure (HF), but we lack an understanding of the underlying pathophysiology. Proteomics evaluation of plasma samples may elucidate potential mechanisms and biomarkers of physical frailty in HF. We aimed to identify plasma proteomic biomarkers that are differentially expressed between physically frail and non physically frail adults with HF. Methods: This was a secondary analysis of a subset of data and plasma samples from a study of frailty among patients with New York Heart Association (NYHA) Functional Classification I-IV HF. Physical frailty was measured using the Frailty Phenotype Criteria. Propensity score matching was used to match pairs of physically frail (n = 20) vs. non-physically frail (n = 20) patients on clinical characteristics. Plasma samples were processed using a sensitive liquid chromatography mass spectrometry platform, utilizing a multiplexed tandem mass tag-labeled quantitative proteomics approach. Differentially expressed proteins were quantified individually using paired t tests with associated log fold change of 0.3 and Fisher’s combined p values. Results: The sample (n = 40) was 62.8±16.9 years old, 58% female, and 55% NYHA Class III/IV. Proteomics analysis revealed 7 proteins differentially expressed using full differential criteria: matrix metalloproteinase-14 was downregulated in frailty, and copine-1, low affinity immunoglobulin gamma Fc region receptor III-A and III-B, probable non-functional immunoglobulin kappa variable 2D-24, glutathione S-transferase Mu 1, and argininosuccinate lyase were upregulated in frailty. Conclusions: Proteomic biomarkers related to the immune system, stress response, and detoxification were differentially expressed between physically frail and non-physically frail adults with HF.

Biomarkers↗

Investigation of U content in J-swipe/PIC samples

This final report documents the results of an evaluation of the U content in J-swipes for the International Atomic Energy Agency (IAEA). J-swipes are manufactured with inked numbers (1–30) and U backgrounds that are considered consistent across different lots and manufacturing times. These characteristics make them ideal for use by IAEA inspectors for pre-inspection check samples to ensure inspectors are not cross-contaminating sites. However, recent work has found elevated U concentrations in the inked numbers compared with the J-swipe material. To determine whether the inked numbers correlate with the U backgrounds, triplicate U content measurements were made on Swipes 1, 2, 11, 22, and 28. Triplicates of each swipe were processed through the standard chemistry used by the Oak Ridge National Laboratory Network of Analytical Laboratories team and analyzed for U content by isotope dilution via multicollector inductively coupled plasma mass spectrometry. Finally, samples were made by mass consisting of only ink areas and only cotton swipe material to determine the trace element differences between the cotton and the ink.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

Angular scattering of protons through ultrathin graphene foils: Application for time-of-flight instrumentation

Space plasma instruments often rely on ultrathin carbon foils for incident ion detection, time-of-flight (TOF) mass spectrometry, and ionization of energetic neutral atoms. Angular scattering and energy loss of ions or neutral atoms in the foil can degrade instrument performance, including sensitivity and mass resolution; thus, there is an ongoing effort to manufacture thinner foils. Using new 3-layer graphene foils manufactured at the Los Alamos National Laboratory, we demonstrate that these are the thinnest foils reported to date and discuss future testing required for application in space instrumentation. We characterize the angular scattering distribution for 3–30 keV protons through the foils, which is used as a proxy for the foil thickness. We show that these foils are ~2.5–4.5 times thinner than the state-of-the-art carbon foils and ~1.6 times thinner than other graphene foils described in the literature. We find that the inverse relationship between angular scattering and energy no longer holds, reaffirming that this may indicate a new domain of beam–foil interactions for ultrathin (few-layer) graphene foils.

47 OTHER INSTRUMENTATION↗

QC-GN 2 oMS 2 : a Graph Neural Net for High Resolution Mass Spectra Prediction

Predicting the mass spectrum of a molecular ion is often accomplished via three generalized approaches: rules-based methods for bond breaking, deep learning, or quantum chemical (QC) modeling. Rules-based approaches are often limited by the conditions for different chemical subspaces and perform poorly under chemical regimes with few defined rules. QC modeling is theoretically robust but requires significant amounts of computational time to produce a spectrum for a given target. Among deep learning techniques, graph neural networks (GNNs) have performed better than previous work with fingerprint-based neural networks in mass spectra prediction. To explore this technique further, we investigate the effects of including quantum chemically derived information as edge features in the GNN to increase predictive accuracy. The models we investigated include categorical bond order, bond force constants derived from extended tight-binding (xTB) quantum chemistry, and acyclic bond dissociation energies. Throughout this work, we evaluated these models against a control GNN with no edge features in the input graphs. Bond dissociation enthalpies yielded the best improvement with a cosine similarity score of 0.462 relative to the baseline model (0.437). In this work we also apply dynamic graph attention which improves performance on benchmark problems and supports the inclusion of edge features. Between implementations, we investigate the nature of the molecular embedding for spectra prediction and discuss the recognition of fragment topographies in distinct chemistries for further development in tandem mass spectrometry prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Greetings from the ASMS Publications Committee

Here, we hope this editorial helps to inspire and provide you with an opportunity to help shape JASMS to suit the needs of each ASMS member. [Editorial at Journal of the American Society for Mass Spectrometry]

99 GENERAL AND MISCELLANEOUS↗

Atmospheric Brown Carbon on the Tibetan Plateau: Regional Differences in Chemical Composition and Light Absorption Properties

In this work, fine particulate matter (PM 2.5 ) filter samples were collected from two high-altitude remote sites located in the southern (QOMS) and northern (WLG) regions of the Tibetan Plateau (TP) to explore the regional differences in brown carbon (BrC) properties. Chemical differences in BrC composition representative of these two areas were inferred from molecular-level analysis of the PM 2.5 samples using high-performance liquid chromatography coupled with photodiode array and high-resolution mass spectrometry detectors. The results show that more polar BrC chromophores were abundant in QOMS samples, while contributions from polar and less polar chromophores were comparable in WLG samples. A higher mass absorption coefficient of BrC was observed at QOMS than at WLG. Strong BrC chromophores in QOMS samples were identified as oxygenated aromatics and nitrophenol compounds, while organosulfate compounds were found in the WLG sample. The results of this study indicate regional differences in BrC chromophores and provide insights into their sources and chemical processes, which should be considered for predictive understanding and modeling of the radiative forcing of aerosol in the TP area.

54 ENVIRONMENTAL SCIENCES↗

High-precision mass measurements of the isomeric and ground states of 44 V: Improving constraints on the isobaric multiplet mass equation parameters of the A=44, 0 + quintet

Background: The quadratic isobaric multiplet mass equation (IMME) has been very successful at predicting the masses of isobaric analog states in the same multiplet, while its coefficients are known to follow specific trends as functions of mass number. The Atomic Mass Evaluation 2016 [Chin. Phys. C 41, 030003 (2017)] 44 V mass value results in an anomalous negative c coefficient for the IMME quadratic term; a consequence of large uncertainty and an unresolved isomeric state. The b and c coefficients can provide useful constraints for construction of the isospin-nonconserving Hamiltonians for the pf shell. In addition, the excitation energy of the 0 + , T = 2 level in 44 V is currently unknown. This state can be used to constrain the mass of the more exotic 44 Cr. Purpose: The aim of the experimental campaign was to perform high-precision mass measurements to resolve the difference between 44 V isomeric and ground states, to test the IMME using the new ground state mass value and to provide necessary ingredients for the future identification of the 0 + , T = 2 state in 44 V. Method: High-precision Penning trap mass spectrometry was performed at LEBIT, located at the National Superconducting Cyclotron Laboratory, to measure the cyclotron frequency ratios of [ 44g,m VO] + versus [ 32 SCO] + , a well-known reference mass, to extract both the isomeric and ground state masses of 44 V. Results: The mass excess of the ground and isomeric states in 44 V were measured to be -23 804.9(80) keV/c 2 and -23 537.0(55) keV/c 2 , respectively. This yielded a new proton separation energy of S p = 1 773(10) keV. Conclusion: The new values of the ground state and isomeric state masses of 44 V have been used to deduce the IMME b and c coefficients of the lowest 2 + and 6 + triplets in A = 44. The 2 + c coefficient is now verified with the IMME trend for lowest multiplets and is in good agreement with the shell-model predictions using charge-dependent Hamiltonians. The mirror energy differences were determined between 44 V and 44 Sc, in line with isospin-symmetry for this multiplet. Finally, the new value of the proton separation energy determined, to an uncertainty of 10 keV, will be important for the determination of the 0 + , T = 2 state in 44 V and, consequently, for prediction of the mass excess of 44 Cr.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A deep generative model enables automated structure elucidation of novel psychoactive substances

Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, in this study, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51% and a top-10 accuracy of 86%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analysed by mass spectrometry.

Cheminformatics↗

NO formation by N 2 /O 2 plasma catalysis: The impact of surface reactions, gas-phase reactions, and mass transport

Pathways and timescales relevant to facilitate plasma-assisted N 2 -O 2 reactions are assessed by measuring the consumption of plasma-derived N and the formation of NO in the gas phase and over Ag catalytic surfaces. These measurements are enabled by a setup that enables N 2 activation in an atmospheric pressure RF plasma jet, enables O 2 addition in the plasma afterglow, facilitates reactions over an Ag wire catalyst, and allows species density quantification by molecular beam mass spectrometry. Gas-phase reactions consume N but do not form NO with high selectivity. The presence of the non-porous Ag wire catalyst increases the rate of N conversion to NO, though mass transfer processes, not surface reactions, dictate the rate of N consumption. When O 2 concentrations and the ratio of the surface area of the catalyst to the void volume of the reactor are high (3–5 mol% O 2 , 10900 m –1 ), N conversion to NO reaches 100 % selectivity. When both N 2 and O 2 are fed through the plasma jet, gas-phase NO production increases 10×, although plasma and gas-phase processes do not exclusively produce NO. Above a threshold NO density, N cannot diffuse to the catalyst surface faster than it is consumed in the gas phase by reactions with NO. Furthermore, the use of heterogeneous catalysts to enhance plasma-driven N x O y formation and control N x O y product selectivity is limited to cases where diffusive transport of N from the gas phase to the catalyst surface is faster than consumption of N from gas-phase reactions with NO.

Engineering↗

Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites

Mass spectrometry analyses have identified tens of thousands of unknown small molecule-associated peaks in different biological specimens. Notably, even the simplest and best studied organisms like Escherichia coli and Saccharomyces cerevisiae yield thousands of unknown peaks. A key question is how many of these reflect actual novel endogenous metabolites. To explore this, Mahieu and Patti used complete 13 C -labeling in E. coli to credential peaks as biological. This reduced the number of unknowns by more than 90%. Here, we carry out similar uniform 13 C-labeling in the Baker’s yeast S. cerevisiae and two less-studied bioenergy-relevant yeasts Rhodotorula toruloides (lipid producer) and Issatchenkia orientalis (organic acid producer). Identification of unknown metabolite peaks and their molecular formulas is facilitated through software tailored for 13 C labeling data and resulting knowledge of carbon atom count. A classification model evaluates the plausibility of each candidate formula, with peaks lacking plausible candidate formulas unlikely to reflect metabolite molecular ions. This approach prioritizes about one hundred candidate abundant unknown metabolites with logical molecular formulas. Most of these are species-specific rather than conserved across yeasts, and more are found in the nonmodel yeasts than S. cerevisiae. Thus, 13 C-labeling data on unknown metabolites highlights the potential for discovering new metabolites and pathways in nonmodel yeasts.

Carbon↗

UCB-GLOBES: An open-access mass spectral database of identified and unidentified atmospheric organic compounds

Chemical characterization of atmospheric organic aerosols using gas chromatography with 70 eV electron ionization mass spectrometry (GC/EI-MS) has been used for decades in advancing molecular marker detection and identification, though primarily through suspect screening and/or targeted analyses. To advance non-targeted analyses of environmental samples, we have catalogued approximately 27 000 mass spectra (MS) of the trimethylsilyl derivatives of semi-volatile organic aerosol (OA) analytes in the open-access University of California Berkeley Goldstein Library of Organic Biogenic Environmental Spectra (UCB-GLOBES). Analytes were observed in ambient samples from the U.S. and the Central Amazon and/or laboratory simulations of secondary OA (SOA) formation. These samples are representative of OA under urban and biomass burning influences as well as SOA derived from biogenic precursors (e.g., isoprene, monoterpenes, sesquiterpenes) and biomass burning intermediates. MS are documented in UCB-GLOBES without regard to known chemical identity, annotated with extensive metadata such as sample source/experimental conditions, any structural information gained from MS analyses, and predicted chemical properties such as average carbon oxidation state and carbon number. UCB-GLOBES MS are compatible for importing into the NIST MS Search program, and we have also provided a Jupyter Notebook for MS visualization and comparisons. We demonstrate the utility of UCB-GLOBES through MS reanalyses of prior analytes observed in ambient data, finding a 20 % reduction in the number of analytes assigned to OA source categories reliant solely on time series correlation and an overall 11 % increase in new MS-based OA source categorization for the Southeast U.S. For 1513 analytes observed previously in the Central Amazon, we found 375 MS matches using UCB-GLOBES vs. 136 MS matches during prior analyses, representing a 14 % gain in newly confirmed or newly categorized OA species. While OA from laboratory oxidation experiments in UCB-GLOBES are highly diverse chemically, on average only 29 % of UCB-GLOBES MS have a mass spectral match to another MS entry in UCB-GLOBES and/or in databases of known compounds (i.e. NIST MS Database, Adams Essential Oil, MANE Flavor and Fragrance Company). This indicates that roughly 70 % of UCB-GLOBES MS are unique thus far, not observed more than once among the laboratory oxidation samples and ambient data in UCB-GLOBES MS. Further, only 18 % can be positively identified using these databases or known authentic standards. This points to a large gap between these laboratory simulations and ambient OA. Overall, the UCB-GLOBES database can be utilized for improving confidence in OA source categorization and/or identification, novel chemical marker discovery, tracking chemical diversity, de novo structure and properties prediction, and improving MS search and matching algorithms. This can ultimately inform future research priorities for the chemical characterization of atmospheric organic samples.

Mass spectrometry↗

Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations

Post-translational modifications regulate the structure and function of proteins that can result in changes to the activity of different pathways. These include modifications altering the redox state of thiol groups on protein cysteine residues, which are sensitive to oxidative environments. While mass spectrometry has advanced the identification of protein thiol modifications and expanded our knowledge of redox-sensitive pathways, the quantitative aspect of this technique is critical for the field of redox proteomics. In this review, we describe how mass spectrometry-based redox proteomics has enabled researchers to accurately quantify the stoichiometry of reversible oxidative modifications on specific cysteine residues of proteins. We will describe advancements in the methodology that allow for the absolute quantitation of thiol modifications, as well as recent reports that have implemented this approach. We will also highlight the significance and application of such measurements and why they are informative for the field of redox biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coherence mapping to identify the intermediates of multi-channel dissociative ionization

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

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.

47 OTHER INSTRUMENTATION↗

A Systematic Investigation of the Effects of Standard-Sample Concentration Mismatch during Fe Isotope Measurement by MC-ICP-MS

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗