A Novel High-Mass Resolution Gas-Source Mass Spectrometer Facility at Ucla

Total Page:16

File Type:pdf, Size:1020Kb

A Novel High-Mass Resolution Gas-Source Mass Spectrometer Facility at Ucla 47th Lunar and Planetary Science Conference (2016) 2238.pdf A NOVEL HIGH-MASS RESOLUTION GAS-SOURCE MASS SPECTROMETER FACILITY AT UCLA. Edward D. Young1, Issaku E. Kohl1, Kaitlyn McCain1, Junko Isa1, and Douglas Rumble III2, 1Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA, USA ([email protected]), 2Geophysical Laboratory, 5251 Broad Branch Rd. NW, Washington DC 20015-1305, USA. Introduction: Gas-source isotope ratio mass spec- Oxygen Isotopes: Analyses of extraterrestrial trometry is one of the primary methods for obtaining samples for precise and accurate 18O/16O and 17O/16O, the highest precision isotope ratio measurements of yielding diagnostic Δ′17O values, has been hampered geological and atmospheric samples. It is the standard historically by the presence of NF+ interfering with 33 + for triple oxygen isotope ratio analysis of meteorites, O2 at mass/charge 33 in the mass spectrum. The for example. However, until very recently, advances Panorama instrument can be used to eliminate this in- in this important technology have been limited. terference by virtue of its high mass resolution (Figure Here we describe a unique and novel isotope ratio 2). In a companion abstract, we demonstrate the ad- mass spectrometer (IRMS), the Nu Instruments Pano- vantages of ground-truthing extraterrestrial oxygen rama, developed explicitly for high-mass-resolution isotope ratio measurements of rocks with this method. analysis of isotopologue ratios of gas samples. We have shown recently that this instrument improves the reliability of oxygen isotope analyses at the highest precision and accuracy. In addition, it offers the pro- spects for developing the foundations for using multi- ply-substituted gas species (CH4, N2, O2) as tracers of atmospheric processes and geochemical cycles that should prove useful for extraterrestrial environments as flight instrumentation (e.g., TILDAS) improves. Panorama: The double-focussing Panorama in- strument (Figure 1) routinely operates at a mass resolv- ing power (MRP) of 40,000 with a maximum useful MRP of ~80,000. The instrument achieves this excep- 33 + + Figure 2. Separation of O2 from NF3 on the tional MRP for a multi-collector using a Matsuda ion Panorama instrument where the latter is shown optical design with an ESA radius of 1018 mm and a schematically at fictively higher ion current for magnetic sector radius of 800 mm. Collectors com- illustration. prise 9 Faraday cups and a single channel of ion count- ing each with continuously variable collector slits. Methane Isotopologues: There is considerable in- Quad 2 terest in the origin and evolution of methane in plane- tary science (e.g., Mars, outer solar system). One Magnet promising new approach for sourcing methane is to (R = 800 mm) measure the excesses or deficits of the multiply- substituted isotopologues relative to the stochastic ref- Oct 1 Hex 2 ESA erence frame. We have used the Panorama to measure (R=1017.6 mm) both 13CH D/12CH and 12CH D /12CH , yielding Quad 1 3 4 2 2 4 Hex 1 9 Faraday Quad 3 13 collectors Δ CH3D and ΔCH2D2, the per mil values relative to ESA the stochastic distribution. In a collaborative effort involving multiple workers, including Barbara Sher- Source Ion counter Gas inlet (20 kV) wood-Lollar, University of Toronto, Giussepe Etiope, Istituto Nazionale di Geofisica e Vulcanologia, and Dionysis Foustoukos, Carnegie Institution of Washing- ton, we are mapping out different sources and sinks of methane in rare-isotopologue space. Results, some of Figure 1. Layout of the Panorama mass spec- which are shown for the first time in Figure 3, show trometer housed at UCLA. promise for using the rare isotopologues of methane as 47th Lunar and Planetary Science Conference (2016) 2238.pdf indicators of reaction pathways, including tempera- rock isotope ratios where analyses can be done in the tures of formation and deviations from thermodynamic gas phase (e.g., oxygen). Future applications include 17 equilibrium. simultaneous measurements of Δ′ O and Δ47 (i.e., temperature of formation) in extraterrestrial car- 15 15 14 bonates. We are also presently measuring N N/ N2 in gas samples. While there are a number of projects related to planetary science in the works, we encourage this community to come with their own ideas for mak- ing use of this new facility (Figure 5). Figure 3. Plot showing the positions of natural and laboratory-produced methane gas in ΔCH2D2 13 vs. Δ CH3D, where here Δ refers to deviations from the stochastic distribution of these rare isotopologues. The curve shows the relationship that holds for thermodynamic equilibrium. Black dots mark temperatures of bond formation in 50 degree increments. Temperatures in italics refer to those of the synthesis experiments. Figure 4. Rare isotopologue effects of mixing two methane samples formed at different temperatures. As shown in Figure 3, laboratory experiments pro- duce significant deviations from equilibrium for CH2D2 that reflect the detailed kinetics of CH4 for- mation. The natural samples shown here yield temper- atures of formation with minimal departures from equi- librium. The measurements shown in Figure 3 are not possible with conventional gas-source isotope ratio mass spectrometers. Sourcing methane can also be complicated by mix- ing. We show the isotope bond-ordering effects (e.g., Figure 3) of mixing two gases with distinct D/H and 13C/12C in Figure 4. There is a tell-tale departure from the equilibrium curve where a mixed source is present. This could be an important tracer of methane for- Figure 5. The Panorama instrument at UCLA. mation and the signatures of such gases can be investi- gated now with an eye towards applications in extrater- Acknowledgements: The Panorama facility was restrial environments in future. funded by the Sloan Foundation’s Deep Carbon Ob- Prospects for Users: We view this unique instru- servatory, the National Science Foundation, the De- ment as providing a proving ground for developing partment of Energy, Shell, UCLA and the Carnegie new tracers of gas formation in planetary atmospheres, Institution. developing new tracers for the origins of volatile ices, and for establishing interference-free measurements of .
Recommended publications
  • Abundances of Isotopologues and Calibration of CO2 Greenhouse Gas Measurements Pieter P
    Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2017-34, 2017 Manuscript under review for journal Atmos. Meas. Tech. Discussion started: 14 February 2017 c Author(s) 2017. CC-BY 3.0 License. Abundances of isotopologues and calibration of CO2 greenhouse gas measurements Pieter P. Tans1,3, Andrew M. Crotwell2,3, and Kirk W. Thoning1,3 1Global Monitoring Division, Earth System Research Laboratory, National Oceanic and Atmospheric 5 Administration, Boulder, Colorado, 80305, USA. 2Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA. 3Central Calibration Laboratory, World Meteorological Organization Global Atmosphere Watch program (WMO/GAW) 10 Correspondence to: Pieter Tans ([email protected]) Abstract We have developed a method to calculate the fractional distribution of CO2 across all of its component isotopologues based on measured δ13C and δ18O values. The fractional distribution can be used with known total CO2 to calculate each component isotopologue individually, in units of mole fraction. The technique is applicable to 15 any molecule where isotopologue-specific values are desired. We used it with a new CO2 calibration system to account for isotopic differences among the primary CO2 standards that define the WMO X2007 CO2 in air calibration scale and between the primary standards and standards in subsequent levels of the calibration hierarchy. The new calibration system uses multiple laser spectroscopic techniques to measure amount of substance fractions 16 12 16 16 13 16 18 12 16 (in mole fraction units) of the three major CO2 isotopologues ( O C O, O C O, and O C O) individually. 20 The three measured values are then combined into total CO2 (accounting for the rare unmeasured isotopologues), 13 18 δ C, and δ O values.
    [Show full text]
  • Detection of Deuterated Methylcyanoacetylene, CH $ 2
    Astronomy & Astrophysics manuscript no. AA202141371_Cabezas ©ESO 2021 June 8, 2021 Detection of deuterated methylcyanoacetylene, CH2DC3N, in TMC-1 ? C. Cabezas1, E. Roueff2, B. Tercero3; 4, M. Agúndez1, N. Marcelino1, P. de Vicente3 and J. Cernicharo1 1 Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain. e-mail: [email protected]; [email protected] 2 LERMA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Universités, 92190 Meudon, France 3 Observatorio Astronómico Nacional (IGN), C/ Alfonso XII, 3, 28014, Madrid, Spain. 4 Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain. Received; accepted ABSTRACT We report the first detection in space of the single deuterated isotopologue of methylcyanoacetylene, CH2DC3N. A total of fifteen rotational transitions, with J = 8-12 and Ka = 0 and 1, were identified for this species in TMC-1 in the 31.0-50.4 GHz range using the Yebes 40m radio telescope. The observed frequencies were used to derive for the first time the spectroscopic parameters of this 10 −2 deuterated isotopologue. We derive a column density of (8:0±0:4)×10 cm . The abundance ratio between CH3C3N and CH2DC3N 13 is ∼22. We also theoretically computed the principal spectroscopic constants of C isotopologues of CH3C3N and CH3C4H and those of the deuterated isotopologues of CH3C4H for which we could expect a similar degree of deuteration enhancement. However, we 13 have not detected either CH2DC4H nor CH3C4D nor any C isotopologue. The different observed deuterium ratios in TMC-1 are reasonably accounted for by a gas phase chemical model where the low temperature conditions favor deuteron transfer through + reactions with H2D .
    [Show full text]
  • Isotopic Fractionation of Carbon, Deuterium, and Nitrogen: a Full Chemical Study?
    A&A 576, A99 (2015) Astronomy DOI: 10.1051/0004-6361/201425113 & c ESO 2015 Astrophysics Isotopic fractionation of carbon, deuterium, and nitrogen: a full chemical study? E. Roueff1;2, J. C. Loison3, and K. M. Hickson3 1 LERMA, Observatoire de Paris, PSL Research University, CNRS, UMR8112, Place Janssen, 92190 Meudon Cedex, France e-mail: [email protected] 2 Sorbonne Universités, UPMC Univ. Paris 6, 4 Place Jussieu, 75005 Paris, France 3 ISM, Université de Bordeaux – CNRS, UMR 5255, 351 cours de la Libération, 33405 Talence Cedex, France e-mail: [email protected] Received 6 October 2014 / Accepted 5 January 2015 ABSTRACT Context. The increased sensitivity and high spectral resolution of millimeter telescopes allow the detection of an increasing number of isotopically substituted molecules in the interstellar medium. The 14N/15N ratio is difficult to measure directly for molecules con- taining carbon. Aims. Using a time-dependent gas-phase chemical model, we check the underlying hypothesis that the 13C/12C ratio of nitriles and isonitriles is equal to the elemental value. Methods. We built a chemical network that contains D, 13C, and 15N molecular species after a careful check of the possible fraction- ation reactions at work in the gas phase. Results. Model results obtained for two different physical conditions that correspond to a moderately dense cloud in an early evolu- tionary stage and a dense, depleted prestellar core tend to show that ammonia and its singly deuterated form are somewhat enriched 15 14 15 + in N, which agrees with observations. The N/ N ratio in N2H is found to be close to the elemental value, in contrast to previous 15 + models that obtain a significant enrichment, because we found that the fractionation reaction between N and N2H has a barrier in + 15 + + 15 + the entrance channel.
    [Show full text]
  • Mass Spectrometric Separation and Quantitation of Overlapping Isotopologues
    Mass Spectrometric Separation and Quantitation of Overlapping Isotopologues. H2O/HOD/D2O and H2Se/HDSe/D2Se Mixtures Juris Meija and Zoltan Mester Institute for National Measurement Standards, National Research Council Canada, Ottawa, Ontario, Canada Alessandro D’Ulivo Laboratory of Instrumental Analytical Chemistry, Institute for Chemical and Physical Processes, Research area of Pisa, National Research Council of Italy, Pisa, Italy Three conceptually different mathematical methods are presented for accurate mass spectro- metric determination of H2O/HOD/D2O and H2Se/HDSe/D2Se concentrations from mix- tures. These are alternating least-squares, weighted two-band target entropy minimization, and a statistical mass balance model. The otherwise nonmeasurable mass spectra of partially deuterated isotopologues (HOD and HDSe) are mathematically constructed. Any recorded isotopologue mixture mass spectra are then deconvoluted by least-squares into their compo- nents. This approach is used to study the H2O/D2O exchange reaction, and is externally validated gravimetrically. The H2O/D2O exchange equilibrium constant is also measured from the deconvoluted 70 eV electron impact GC/MS data (K ϭ 3.85 Ϯ 0.03). (J Am Soc Mass Spectrom 2006, 17, 1028–1036) © 2006 American Society for Mass Spectrometry ` ϩ sotopologues are compounds that differ in isotopic rapid isotope-exchange equilibrium 2HOD H2O composition only, such as H2O and D2O. These com- D2O. Ipounds play an important role in analytical chemistry, Using the best available commercial high-resolution especially in quantitative analysis where most of the mass spectrometers, one can possibly address the H2O/ ⌬ Ͼ modern internal quantitation methods are based on isoto- HOD/D2O system (requiring m/ m 12,000 to fully ϩ ·ϩ pologues.
    [Show full text]
  • Automatic Isotopologue Normalization for Metabolic Tracer Analysis Sophie Trefely1,2* , Peter Ashwell1 and Nathaniel W
    Trefely et al. BMC Bioinformatics (2016) 17:485 DOI 10.1186/s12859-016-1360-7 SOFTWARE Open Access FluxFix: automatic isotopologue normalization for metabolic tracer analysis Sophie Trefely1,2* , Peter Ashwell1 and Nathaniel W. Snyder1 Abstract Background: Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [13C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals. Results: Here we present FluxFix (http://fluxfix.science), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. ‘Unlabeled’ data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions.
    [Show full text]
  • Hydrogen Isotope Exchanges Between Water and Methanol in Interstellar Ices a Faure, M Faure, P Theulé, E Quirico, B Schmitt
    Hydrogen isotope exchanges between water and methanol in interstellar ices A Faure, M Faure, P Theulé, E Quirico, B Schmitt To cite this version: A Faure, M Faure, P Theulé, E Quirico, B Schmitt. Hydrogen isotope exchanges between water and methanol in interstellar ices. Astronomy and Astrophysics - A&A, EDP Sciences, 2015, 584, pp.A98. 10.1051/0004-6361/201526499. hal-01452286 HAL Id: hal-01452286 https://hal.archives-ouvertes.fr/hal-01452286 Submitted on 1 Feb 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A&A 584, A98 (2015) Astronomy DOI: 10.1051/0004-6361/201526499 & c ESO 2015 Astrophysics Hydrogen isotope exchanges between water and methanol in interstellar ices A. Faure1,2,M.Faure1,2, P. Theulé3, E. Quirico1,2, and B. Schmitt1,2 1 Univ. Grenoble Alpes, IPAG, 38000 Grenoble, France e-mail: [email protected] 2 CNRS, IPAG, 38000 Grenoble, France 3 Aix-Marseille Université, PIIM UMR-CNRS 7345, 13397 Marseille, France Received 8 May 2015 / Accepted 22 September 2015 ABSTRACT The deuterium fractionation of gas-phase molecules in hot cores is believed to reflect the composition of interstellar ices.
    [Show full text]
  • Computational and Statistical Methods for Mass Spectrometry Data Analysis
    University of Warsaw Faculty of Mathematics, Informatics and Mechanics Mateusz Krzysztof Łąi Student no. Computational and Statistical Methods for Mass Spectrometry Data Analysis PhD’s dissertation in COMPUTER SCIENCE Supervisors: Prof. Anna Gambin Institute of Informatics, University of Warsaw Dr Błażej Miasojedow Institute of Applied Mathematics, University of Warsaw September Supervisor’s statement Hereby I confirm that the presented thesis was prepared under my supervi- sion and that it fulfils the requirements for the degree of PhD of Computer Science. Date Supervisor’s signature Author’s statement Hereby I declare that the presented thesis was prepared by me and none of its contents was obtained by means that are against the law. The thesis has never before been a subject of any procedure of obtaining an academic degree. Moreover, I declare that the present version of the thesis is identical to the attached electronic version. Date Author’s signature Abstract Computational and Statistical Methods for Mass Spectrometry Data Analysis This dissertation covers a series of related topics in the mathematical modelling of mass spectrometry data. The dissertation opens by a presentation of an optimal al- gorithm for the generation of the fine isotopic structure. We further show the ap- plications of that algorithm to the problem of deconvoluting mixed isotopic signals, in two different ways. We also approach the problem of estimating the deep pa- rameters of mass detectors, estimating the parameters of a function that relates the instrument-generated intensities to the numbers of ions. These solutions are applied to the problem of understanding Electron Driven reactions, whose principal aim is to induce ion fragmentation and, in that way, enhance the instrument’s identifica- tion capabilities.
    [Show full text]
  • Position-Specific Hydrogen Isotope Equilibrium in Propane
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Caltech Authors Accepted Manuscript Position-Specific Hydrogen Isotope Equilibrium in Propane Hao Xie, Camilo Ponton, Michael J Formolo, Michael Lawson, Brian K Peterson, Max K. Lloyd, Alex L Sessions, John M Eiler PII: S0016-7037(18)30340-5 DOI: https://doi.org/10.1016/j.gca.2018.06.025 Reference: GCA 10814 To appear in: Geochimica et Cosmochimica Acta Received Date: 25 January 2018 Revised Date: 18 June 2018 Accepted Date: 22 June 2018 Please cite this article as: Xie, H., Ponton, C., Formolo, M.J., Lawson, M., Peterson, B.K., Lloyd, M.K., Sessions, A.L., Eiler, J.M., Position-Specific Hydrogen Isotope Equilibrium in Propane, Geochimica et Cosmochimica Acta (2018), doi: https://doi.org/10.1016/j.gca.2018.06.025 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Position-Specific Hydrogen Isotope Equilibrium in Propane Hao Xie1*, Camilo Ponton1, Michael J Formolo2, Michael Lawson3, Brian K Peterson4, Max K. Lloyd1, Alex L Sessions1, John M Eiler1 1. Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA 2.
    [Show full text]
  • Stable Water Isotopologues in the Stratosphere Retrieved from Odin/SMR Measurements
    remote sensing Article Stable Water Isotopologues in the Stratosphere Retrieved from Odin/SMR Measurements Tongmei Wang 1,2,* ID , Qiong Zhang 1, Stefan Lossow 3,Léon Chafik 4, Camille Risi 5, Donal Murtagh 6 and Abdel Hannachi 2 1 Department of Physical Geography, Stockholm University, 10691 Stockholm, Sweden; [email protected] 2 Department of Meteorology, Stockholm University, 10691 Stockholm, Sweden; [email protected] 3 Institute for Meteorology and Climate Research, Karlsruhe Institute of Technology, 76021 Leopoldshafen, Germany; [email protected] 4 Geophysical Institute, Bjerknes Center for Climate Research, University of Bergen, 5020 Bergen, Norway; leonchafi[email protected] 5 LMD/IPSL, CNRS, 75005 Paris, France; [email protected] 6 Department of Earth and Space Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden; [email protected] * Correspondence: [email protected]; Tel.: +46-08-162403 Received: 16 November 2017; Accepted: 23 January 2018; Published: 25 January 2018 Abstract: Stable Water Isotopologues (SWIs) are important diagnostic tracers for understanding processes in the atmosphere and the global hydrological cycle. Using eight years (2002–2009) of retrievals from Odin/SMR (Sub-Millimetre Radiometer), the global climatological features of 16 18 18 three SWIs, H2 O, HDO and H2 O, the isotopic composition δD and δ O in the stratosphere are analysed for the first time. Spatially, SWIs are found to increase with altitude due to stratospheric methane oxidation. In the tropics, highly depleted SWIs in the lower stratosphere indicate the effect of dehydration when the air comes through the cold tropopause, while, at higher latitudes, more enriched SWIs in the upper stratosphere during summer are produced and transported to the other hemisphere via the Brewer–Dobson circulation.
    [Show full text]
  • Stable Isotopes – Terminology 1 2
    Outline Key questions to answer after this lecture: Stable Isotopes – Terminology 1) Definitions and terminology Roland A. Werner What is an isotope ? Institut für Agrarwissenschaften, ETH Zürich 2) Properties and isotope fractionation What properties differ between isotopic variants ? How does this influence reaction rates ? 3) Calculating and describing isotope fractionation How can I calculate and describe isotope fractionation ? What pitfalls and approximation should I be aware of ? 15st January 2021, 2 1 2 Part 1 Definition Isotope . Greek isos = "equal", tópos = "site, place" Isotopes occupy the same position in the periodic table of elements . Isotopes of an element have nuclei with the same number of protons (atomic number) but different numbers of neutrons . Therefore, isotopes have different masses and different nuclear properties Mass number m Element Atomic number n E 15st January 2021, 3 15st January 2021, 4 3 4 1 Definition Isotope Definition Isotope . Same position in periodic table Atom Core Mass number . Same number of protons (atomic number) but 6- 6- Hull different numbers of neutrons 6+ 6+ . Therefore, isotopes have different masses (mass 6n 7n number) and different nuclear properties 6 protons and 6 protons and Atomic number 7 neutrons 6 neutrons 12 13 Atoms with a (higher) number of neutrons C C 13 6 6 C can be used (one or more) than protons for NMR Different atomic weight 6 protons 15st January 2021, 5 15st January 2021, 6 5 6 Definition Isotope Definition Stable / Radioactive Isotope Atom Core Stable isotope or radioactive isotope ? Mass number 6- 6- Hull If the ratio of protons to neutrons in the nuclide of an atom is unbalanced, the atom is instable and decays 6+ 6+ under emission of radiation.
    [Show full text]
  • Correcting for Naturally Occurring Mass Isotopologue Abundances in Stable-Isotope Tracing Experiments with Polymid
    H OH metabolites OH Article Correcting for Naturally Occurring Mass Isotopologue Abundances in Stable-Isotope Tracing Experiments with PolyMID Heesoo Jeong 1, Yan Yu 2, Henrik J. Johansson 3, Frank C. Schroeder 2, Janne Lehtiö 3 and Nathaniel M. Vacanti 1,3,* 1 Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA; [email protected] 2 Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; [email protected] (Y.Y.); [email protected] (F.C.S.) 3 Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 17165 Solna, Sweden; [email protected] (H.J.J.); [email protected] (J.L.) * Correspondence: [email protected] Abstract: Stable-isotope tracing is a method to measure intracellular metabolic pathway utilization by feeding a cellular system a stable-isotope-labeled tracer nutrient. The power of the method to resolve differential pathway utilization is derived from the enrichment of metabolites in heavy isotopes that are synthesized from the tracer nutrient. However, the readout is complicated by the presence of naturally occurring heavy isotopes that are not derived from the tracer nutrient. Herein we present an algorithm, and a tool that applies it (PolyMID-Correct, part of the PolyMID software package), to computationally remove the influence of naturally occurring heavy isotopes. Citation: Jeong, H.; Yu, Y.; Johansson, The algorithm is applicable to stable-isotope tracing data collected on low- and high- mass resolution H.J.; Schroeder, F.C.; Lehtiö, J.; mass spectrometers. PolyMID-Correct is open source and available under an MIT license. Vacanti, N.M.
    [Show full text]
  • Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane
    Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane Jonathan Gropp1,*, Mark A. Iron2, and Itay Halevy1 1Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel 2Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel *Corresponding author, E-mail address: [email protected] (J. Gropp) Abstract Microbial production and consumption of methane are widespread in natural and ar- tificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to identify its sources are complicated by incom- plete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracel- lular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but esti- mates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (13C/12C) and hydrogen (D/H) isotopes among compounds in the anaerobic methane metabolisms, as well as the abundance of double isotope substitutions (\clumping," i.e., a single 13C{D bond or two 12C{D bonds) in these compounds. The density functional theory calcu- lations are at the M06-L/def2-TZVP level of theory with the SMD implicit solvation model, which we have recently tested against measured equilibrium isotope fractiona- tions. The computed 13β and 2β values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment in 13C and D of the molecules with more oxidized carbon.
    [Show full text]