We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data ...analysis workflows that offers ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section (CCS) calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation; algorithm implementations simultaneously utilize all dimensions to (i) offer greater separation between features, thus improving detection sensitivity, (ii) increase alignment/feature matching confidence among data sets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS metabolomics data to illustrate the advantages of a multidimensional approach in each data processing step.
Mass Spectrometry Adduct Calculator Blumer, Madison R; Chang, Christine H; Brayfindley, Evangelina ...
Journal of chemical information and modeling,
12/2021, Letnik:
61, Številka:
12
Journal Article
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We describe the Mass Spectrometry Adduct Calculator (MSAC), an automated Python tool to calculate the adduct ion masses of a parent molecule. Here, adduct refers to a version of a parent molecule M ...that is charged due to addition or loss of atoms and electrons resulting in a charged ion, for example, M + H+. MSAC includes a database of 147 potential adducts and adduct/neutral loss combinations and their mass-to-charge ratios (m/z) as extracted from the NIST/EPA/NIH Mass Spectral Library (NIST17), Global Natural Products Social Molecular Networking Public Spectral Libraries (GNPS), and MassBank of North America (MoNA). The calculator relies on user-selected subsets of the combined database to calculate expected m/z for adducts of molecules supplied as formulas. This tool is intended to help researchers create identification libraries to collect evidence for the presence of molecules in mass spectrometry data. While the included adduct database focuses on adducts typically detected during liquid chromatography–mass spectrometry analyses, users may supply their own lists of adducts and charge states for calculating expected m/z. We also analyzed statistics on adducts from spectra contained in the three selected mass spectral libraries. MSAC is freely available at https://github.com/pnnl/MSAC.
The frequency dependence of radio pulse arrival times provides a probe of structures in the intervening media. Demorest et al. was the first to show a short-term (∼100-200 days) reduction in the ...electron content along the line of sight to PSR J1713+0747 in data from 2008 (approximately MJD 54750) based on an apparent dip in the dispersion measure of the pulsar. We report on a similar event in 2016 (approximately MJD 57510), with average residual pulse-arrival times −3.0, −1.3, and −0.7 s at 820, 1400, and 2300 MHz, respectively. Timing analyses indicate possible departures from the standard −2 dispersive-delay dependence. We discuss and rule out a wide variety of potential interpretations. We find the likeliest scenario to be lensing of the radio emission by some structure in the interstellar medium, which causes multiple frequency-dependent pulse arrival-time delays.
Boreal peatlands are important global carbon reservoirs that are particularly vulnerable to predicted climate changes such as increasing CO2 and temperature. Since microbial activities regulate the ...balance of carbon sequestered into soil organic matter or remineralized to CO2, characterizing their response to these environmental factors is critical to predicting how peatland ecosystems will affect climate-carbon cycle feedbacks. Here we examined in-situ taxon-specific variation in microbial growth under long-term elevated CO2 and across a gradient of warming treatments in a northern Minnesota peat bog using quantitative stable isotope probing with 18O-water. Across temperatures, bacterial taxa were grouped according to the excess atom fraction 18O (EAF) of their genomes, a proxy for DNA replication and hence, growth. Taxon-specific growth across CO2 and temperature treatments clustered into relatively few response patterns. While a large portion of taxa showed little to no growth under ambient CO2, many of the same taxa grew rapidly under elevated CO2. We found support for phylogenetic conservation of response patterns among Acidobacteria and Proteobacteria, the two most abundant phyla in our data. Our results suggest certain taxa may be primed for new climate conditions and have a greater influence on carbon cycling with implications for future climate mitigation strategies.
Abstract The millisecond pulsar J1713+0747 underwent a sudden and significant pulse shape change between 2021 April 16 and 17 (MJDs 59320 and 59321). Subsequently, the pulse shape gradually recovered ...over the course of several months. We report the results of continued multifrequency radio observations of the pulsar made using the Canadian Hydrogen Intensity Mapping Experiment and the 100 m Green Bank Telescope in a 3 yr period encompassing the shape change event, between 2020 February and 2023 February. As of 2023 February, the pulse shape had returned to a state similar to that seen before the event, but with measurable changes remaining. The amplitude of the shape change and the accompanying time-of-arrival residuals display a strong nonmonotonic dependence on radio frequency, demonstrating that the event is neither a glitch (the effects of which should be independent of radio frequency, ν ) nor a change in dispersion measure alone (which would produce a delay proportional to ν −2 ). However, it does bear some resemblance to the two previous “chromatic timing events” observed in J1713+0747, as well as to a similar event observed in PSR J1643−1224 in 2015.
We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data ...analysis workflows that offers ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section (CCS) calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation; algorithm implementations simultaneously utilize all dimensions to (i) offer greater separation between features, thus improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS data to illustrate the advantages of a multidimensional approach in each data processing step.
The frequency dependence of radio pulse arrival times provides a probe of structures in the intervening media. Demorest et al. 2013 was the first to show a short-term (~100-200 days) reduction in the ...electron content along the line of sight to PSR J1713+0747 in data from 2008 (approximately MJD 54750) based on an apparent dip in the dispersion measure of the pulsar. We report on a similar event in 2016 (approximately MJD 57510), with average residual pulse-arrival times of approximately 3.0,-1.3, and -0.7 microseconds at 820, 1400, and 2300 MHz, respectively. Timing analyses indicate possible departures from the standard nu^-2 dispersive-delay dependence. We discuss and rule out a wide variety of potential interpretations. We find the likeliest scenario to be lensing of the radio emission by some structure in the interstellar medium, which causes multiple frequency-dependent pulse arrival-time delays.
The millisecond pulsar J1713+0747 underwent a sudden and significant pulse shape change between April 16 and 17, 2021 (MJDs 59320 and 59321). Subsequently, the pulse shape gradually recovered over ...the course of several months. We report the results of continued multi-frequency radio observations of the pulsar made using the Canadian Hydrogen Intensity Mapping Experiment (CHIME) and the 100-meter Green Bank Telescope (GBT) in a three-year period encompassing the shape change event, between February 2020 and February 2023. As of February 2023, the pulse shape had returned to a state similar to that seen before the event, but with measurable changes remaining. The amplitude of the shape change and the accompanying TOA residuals display a strong non-monotonic dependence on radio frequency, demonstrating that the event is neither a glitch (the effects of which should be independent of radio frequency, \(\nu\)) nor a change in dispersion measure (DM) alone (which would produce a delay proportional to \(\nu^{-2}\)). However, it does bear some resemblance to the two previous "chromatic timing events" observed in J1713+0747 (Demorest et al. 2013; Lam et al. 2016), as well as to a similar event observed in PSR J1643-1224 in 2015 (Shannon et al. 2016).
Boreal peatlands are important global carbon reservoirs that are vulnerable to increasing CO2 and associated warming. Soil microbes regulate the balance of carbon that is stored in peat or ...remineralized to CO2; so characterizing microbial responses to warming and rising CO2 is critical to predicting how peatlands will feed back to ongoing climate change. To address microbiome responses to changing climate, we examined taxon-specific bacterial growth under elevated CO2 and across a warming gradient in a peatland using 18O-water quantitative stable isotope probing. Using in situ temperatures, we clustered the responses of bacterial taxa according to excess atom fraction 18O of their genomes, a proxy for growth. Many taxa that showed little to no growth across the temperature range under ambient CO2 grew rapidly at certain temperatures under elevated CO2, highlighting a strong interplay between warming and CO2 concentrations. The temperature of maximum growth for Proteobacteria shifted higher under elevated CO2, while that of Acidobacteria shifted lower. We found support for phylogenetic conservation of growth patterns among Acidobacteria and Proteobacteria under ambient, but not elevated CO2. Our results suggest that certain taxa may be predisposed for growth under altered climate conditions, with a disproportionate influence on carbon cycling and peatland feedbacks to climate change.
•Elevated CO2 with increased temperature modifies bacterial growth.•Taxa that showed little to no growth under ambient CO2 grew rapidly under eCO2.•Proteobacteria and Actinobacteria appear poised to benefit from climate shifts.
We search for an isotropic stochastic gravitational-wave background (GWB) in the \(12.5\)-year pulsar timing data set collected by the North American Nanohertz Observatory for Gravitational Waves. ...Our analysis finds strong evidence of a stochastic process, modeled as a power-law, with common amplitude and spectral slope across pulsars. The Bayesian posterior of the amplitude for an \(f^{-2/3}\) power-law spectrum, expressed as the characteristic GW strain, has median \(1.92 \times 10^{-15}\) and \(5\%\)--\(95\%\) quantiles of \(1.37\)--\(2.67 \times 10^{-15}\) at a reference frequency of \(f_\mathrm{yr} = 1 ~\mathrm{yr}^{-1}\). The Bayes factor in favor of the common-spectrum process versus independent red-noise processes in each pulsar exceeds \(10,000\). However, we find no statistically significant evidence that this process has quadrupolar spatial correlations, which we would consider necessary to claim a GWB detection consistent with general relativity. We find that the process has neither monopolar nor dipolar correlations, which may arise from, for example, reference clock or solar system ephemeris systematics, respectively. The amplitude posterior has significant support above previously reported upper limits; we explain this in terms of the Bayesian priors assumed for intrinsic pulsar red noise. We examine potential implications for the supermassive black hole binary population under the hypothesis that the signal is indeed astrophysical in nature.
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