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Gessler A, Wieloch T, Saurer M, Lehmann MM, Werner RA, Kammerer B. The marriage between stable isotope ecology and plant metabolomics - new perspectives for metabolic flux analysis and the interpretation of ecological archives. THE NEW PHYTOLOGIST 2024; 244:21-31. [PMID: 39021246 DOI: 10.1111/nph.19973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.
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Affiliation(s)
- Arthur Gessler
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
- Ecosystem Ecology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Thomas Wieloch
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, 90736, Umeå, Sweden
| | - Matthias Saurer
- Ecosystem Ecology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Marco M Lehmann
- Ecosystem Ecology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Roland A Werner
- Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Bernd Kammerer
- Core Competence Metabolomics, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
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2
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Boros LG, Seneff S, Túri M, Palcsu L, Zubarev RA. Active involvement of compartmental, inter- and intramolecular deuterium disequilibrium in adaptive biology. Proc Natl Acad Sci U S A 2024; 121:e2412390121. [PMID: 39213185 PMCID: PMC11406250 DOI: 10.1073/pnas.2412390121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Affiliation(s)
- László G Boros
- Department of Physics and Astronomy, Physics of Living Systems, Sub-Molecular Medical Sciences Deutenomics Core, Vrije University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Stephanie Seneff
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Marianna Túri
- Isotope Climatology and Environmental Research Centre, Hungarian Research Network Institute for Nuclear Research, Debrecen H-4001, Hungary
| | - László Palcsu
- Isotope Climatology and Environmental Research Centre, Hungarian Research Network Institute for Nuclear Research, Debrecen H-4001, Hungary
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
- Department of Pharmacological & Technological Chemistry, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- The National Medical Research Center for Endocrinology, Moscow 117292, Russia
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3
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Kantnerová K, Kuhlbusch N, Juchelka D, Hilkert A, Kopf S, Neubauer C. A guide to precise measurements of isotope abundance by ESI-Orbitrap MS. Nat Protoc 2024; 19:2435-2466. [PMID: 38654136 DOI: 10.1038/s41596-024-00981-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/08/2024] [Indexed: 04/25/2024]
Abstract
Stable isotopes of carbon, hydrogen, nitrogen, oxygen and sulfur are widespread in nature. Nevertheless, their relative abundance is not the same everywhere. This is due to kinetic isotope effects in enzymes and other physical principles such as equilibrium thermodynamics. Variations in isotope ratios offer unique insights into environmental pollution, trophic relationships in ecology, metabolic disorders and Earth history including climate history. Although classical isotope ratio mass spectrometry (IRMS) techniques still struggle to access intramolecular information like site-specific isotope abundance, electrospray ionization-Orbitrap mass spectrometry can be used to achieve precise and accurate intramolecular quantification of isotopically substituted molecules ('isotopocules'). This protocol describes two procedures. In the first one, we provide a step-by-step beginner's guide for performing multi-elemental, intramolecular and site-specific stable isotope analysis in unlabeled polar solutes by direct infusion. Using a widely available calibration solution, isotopocules of trifluoroacetic acid and immonium ions from the model peptide MRFA are quantified. In the second approach, nitrate is used as a simple model for a flow injection routine that enables access to a diverse range of naturally occurring isotopic signatures in inorganic oxyanions. Each procedure takes 2-3 h to complete and requires expertise only in general mass spectrometry. The workflows use optimized Orbitrap IRMS data-extraction and -processing software and are transferable to various analytes amenable to soft ionization, including metabolites, peptides, drugs and environmental pollutants. Optimized mass spectrometry systems will enable intramolecular isotope research in many areas of biology.
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Affiliation(s)
- Kristýna Kantnerová
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA
| | - Nils Kuhlbusch
- Thermo Fisher Scientific GmbH, Bremen, Germany
- University of Münster, Münster, Germany
| | | | | | - Sebastian Kopf
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA
| | - Cajetan Neubauer
- University of Colorado Boulder & Institute for Arctic and Alpine Research (INSTAAR), Boulder, CO, USA.
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4
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Qu J, Xu Y, Zhao S, Xiong L, Jing J, Lui S, Huang J, Shi H. The biological impact of deuterium and therapeutic potential of deuterium-depleted water. Front Pharmacol 2024; 15:1431204. [PMID: 39104389 PMCID: PMC11298373 DOI: 10.3389/fphar.2024.1431204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
Since its discovery by Harold Urey in 1932, deuterium has attracted increased amounts of attention from the scientific community, with many previous works aimed to uncover its biological effects on living organisms. Existing studies indicate that deuterium, as a relatively rare isotope, is indispensable for maintaining normal cellular function, while its enrichment and depletion can affect living systems at multiple levels, including but not limited to molecules, organelles, cells, organs, and organisms. As an important compound of deuterium, deuterium-depleted water (DDW) possess various special effects, including but not limited to altering cellular metabolism and potentially inhibiting the growth of cancer cells, demonstrating anxiolytic-like behavior, enhancing long-term memory in rats, reducing free radical oxidation, regulating lipid metabolism, harmonizing indices related to diabetes and metabolic syndrome, and alleviating toxic effects caused by cadmium, manganese, and other harmful substances, implying its tremendous potential in anticancer, neuroprotective, antiaging, antioxidant, obesity alleviation, diabetes and metabolic syndrome treatment, anti-inflammatory, and detoxification, thereby drawing extensive attention from researchers. This review comprehensively summarizes the latest progress in deuterium acting on living organisms. We start by providing a snapshot of the distribution of deuterium in nature and the tolerance of various organisms to it. Then, we discussed the impact of deuterium excess and deprivation, in the form of deuterium-enriched water (DEW) and deuterium-depleted water (DDW), on living organisms at different levels. Finally, we focused on the potential of DDW as an adjuvant therapeutic agent for various diseases and disorders.
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Affiliation(s)
- Jiao Qu
- Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Yufei Xu
- Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Shuang Zhao
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Xiong
- Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jing Jing
- Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Su Lui
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Juan Huang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Institute of Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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5
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Boros LG, Kyriakopoulos AM, Brogna C, Piscopo M, McCullough PA, Seneff S. Long-lasting, biochemically modified mRNA, and its frameshifted recombinant spike proteins in human tissues and circulation after COVID-19 vaccination. Pharmacol Res Perspect 2024; 12:e1218. [PMID: 38867495 PMCID: PMC11169277 DOI: 10.1002/prp2.1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/20/2024] [Indexed: 06/14/2024] Open
Abstract
According to the CDC, both Pfizer and Moderna COVID-19 vaccines contain nucleoside-modified messenger RNA (mRNA) encoding the viral spike glycoprotein of severe acute respiratory syndrome caused by corona virus (SARS-CoV-2), administered via intramuscular injections. Despite their worldwide use, very little is known about how nucleoside modifications in mRNA sequences affect their breakdown, transcription and protein synthesis. It was hoped that resident and circulating immune cells attracted to the injection site make copies of the spike protein while the injected mRNA degrades within a few days. It was also originally estimated that recombinant spike proteins generated by mRNA vaccines would persist in the body for a few weeks. In reality, clinical studies now report that modified SARS-CoV-2 mRNA routinely persist up to a month from injection and can be detected in cardiac and skeletal muscle at sites of inflammation and fibrosis, while the recombinant spike protein may persist a little over half a year in blood. Vaccination with 1-methylΨ (pseudouridine enriched) mRNA can elicit cellular immunity to peptide antigens produced by +1 ribosomal frameshifting in major histocompatibility complex-diverse people. The translation of 1-methylΨ mRNA using liquid chromatography tandem mass spectrometry identified nine peptides derived from the mRNA +1 frame. These products impact on off-target host T cell immunity that include increased production of new B cell antigens with far reaching clinical consequences. As an example, a highly significant increase in heart muscle 18-flourodeoxyglucose uptake was detected in vaccinated patients up to half a year (180 days). This review article focuses on medical biochemistry, proteomics and deutenomics principles that explain the persisting spike phenomenon in circulation with organ-related functional damage even in asymptomatic individuals. Proline and hydroxyproline residues emerge as prominent deuterium (heavy hydrogen) binding sites in structural proteins with robust isotopic stability that resists not only enzymatic breakdown, but virtually all (non)-enzymatic cleavage mechanisms known in chemistry.
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Affiliation(s)
- László G. Boros
- Sub‐Molecular Medical Sciences Deutenomics CoreVrije University AmsterdamAmsterdamThe Netherlands
| | | | - Carlo Brogna
- Department of ResearchCraniomed Group Facility SrlItaly
| | - Marina Piscopo
- Department of BiologyUniversity of Naples Federico IINaplesItaly
| | | | - Stephanie Seneff
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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6
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Silverman SN, Wijker RS, Sessions AL. Biosynthetic and catabolic pathways control amino acid δ 2H values in aerobic heterotrophs. Front Microbiol 2024; 15:1338486. [PMID: 38646628 PMCID: PMC11026604 DOI: 10.3389/fmicb.2024.1338486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/20/2024] [Indexed: 04/23/2024] Open
Abstract
The hydrogen isotope ratios (δ2HAA values) of amino acids in all organisms are substantially fractionated relative to growth water. In addition, they exhibit large variations within microbial biomass, animals, and human tissues, hinting at rich biochemical information encoded in such signals. In lipids, such δ2H variations are thought to primarily reflect NADPH metabolism. Analogous biochemical controls for amino acids remain largely unknown, but must be elucidated to inform the interpretation of these measurements. Here, we measured the δ2H values of amino acids from five aerobic, heterotrophic microbes grown on different carbon substrates, as well as five Escherichia coli mutant organisms with perturbed NADPH metabolisms. We observed similar δ2HAA patterns across all organisms and growth conditions, which-consistent with previous hypotheses-suggests a first-order control by biosynthetic pathways. Moreover, δ2HAA values varied systematically with the catabolic pathways activated for substrate degradation, with variations explainable by the isotopic compositions of important cellular metabolites, including pyruvate and NADPH, during growth on each substrate. As such, amino acid δ2H values may be useful for interrogating organismal physiology and metabolism in the environment, provided we can further elucidate the mechanisms underpinning these signals.
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Affiliation(s)
- Shaelyn N. Silverman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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7
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Zhang X, Meng Z, Beusch CM, Gharibi H, Cheng Q, Lyu H, Di Stefano L, Wang J, Saei AA, Végvári Á, Gaetani M, Zubarev RA. Ultralight Ultrafast Enzymes. Angew Chem Int Ed Engl 2024; 63:e202316488. [PMID: 38009610 DOI: 10.1002/anie.202316488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.
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Affiliation(s)
- Xuepei Zhang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Christian M Beusch
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hezheng Lyu
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Luciano Di Stefano
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Jijing Wang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Amir A Saei
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177, Stockholm, Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab), 17177, Stockholm, Sweden
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- >Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146, Moscow, Russia
- The National Medical Research Center for Endocrinology, Moskva, 115478 Moscow, Russia
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8
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Di Martino RMC, Maxwell BD, Pirali T. Deuterium in drug discovery: progress, opportunities and challenges. Nat Rev Drug Discov 2023; 22:562-584. [PMID: 37277503 PMCID: PMC10241557 DOI: 10.1038/s41573-023-00703-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 06/07/2023]
Abstract
Substitution of a hydrogen atom with its heavy isotope deuterium entails the addition of one neutron to a molecule. Despite being a subtle change, this structural modification, known as deuteration, may improve the pharmacokinetic and/or toxicity profile of drugs, potentially translating into improvements in efficacy and safety compared with the non-deuterated counterparts. Initially, efforts to exploit this potential primarily led to the development of deuterated analogues of marketed drugs through a 'deuterium switch' approach, such as deutetrabenazine, which became the first deuterated drug to receive FDA approval in 2017. In the past few years, the focus has shifted to applying deuteration in novel drug discovery, and the FDA approved the pioneering de novo deuterated drug deucravacitinib in 2022. In this Review, we highlight key milestones in the field of deuteration in drug discovery and development, emphasizing recent and instructive medicinal chemistry programmes and discussing the opportunities and hurdles for drug developers, as well as the questions that remain to be addressed.
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Affiliation(s)
| | | | - Tracey Pirali
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy.
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9
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Gharibi H, Chernobrovkin AL, Saei AA, Zhang X, Gaetani M, Makarov AA, Zubarev RA. Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides. Anal Chem 2022; 94:15048-15056. [PMID: 36251694 PMCID: PMC9631351 DOI: 10.1021/acs.analchem.2c03119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Measuring the relative abundances of heavy stable isotopes of the elements C, H, N, and O in proteins is of interest in environmental science, archeology, zoology, medicine, and other fields. The isotopic abundance measurements of the fine structure of immonium ions with ultrahigh resolution mass spectrometry obtained in gas-phase fragmentation of polypeptides have previously uncovered anomalous deuterium enrichment in (hydroxy)proline of bone collagen in marine mammals. Here, we provide a detailed description and validation of this approach and demonstrate per mil-range precision of isotopic ratio measurements in aliphatic residues from proteins and cell lysates. The analysis consists of proteomics-type experiment demanding sub-microgram amounts of a protein sample and providing concomitantly protein sequence data allowing one to verify sample purity and establish its identity. A novel software tool protein amino acid-resolved isotopic ratio mass spectrometry (PAIR-MS) is presented for extracting isotopic ratio data from the raw data files acquired on an Orbitrap mass spectrometer.
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Affiliation(s)
- Hassan Gharibi
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
| | | | - Amir Ata Saei
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Department
of Cell Biology, Harvard Medical School, Boston, Massachusetts02115, United States
| | - Xuepei Zhang
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Chemical
Proteomics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Unit
of Chemical Proteomics, Science for Life
Laboratory (SciLifeLab), Stockholm171 77, Sweden
| | - Massimiliano Gaetani
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Chemical
Proteomics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Unit
of Chemical Proteomics, Science for Life
Laboratory (SciLifeLab), Stockholm171 77, Sweden
| | | | - Roman A. Zubarev
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Stockholm171 77, Sweden
- Department
of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow119146, Russia
- The
National Medical Research Center for Endocrinology, 115478Moscow, Russia
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