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Kostyukevich Y, Osipenko S, Borisova L, Kireev A. In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions. J Mass Spectrom 2024; 59:e5032. [PMID: 38736146 DOI: 10.1002/jms.5032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSn fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS5 level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at -COOH group, the eliminating hydrogen always comes from -NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the -NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.
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Affiliation(s)
| | - Sergey Osipenko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Albert Kireev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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Osipenko S, Bashilov A, Vishnevskaya A, Rumiantseva L, Levashova A, Kovalenko A, Tupertsev B, Kireev A, Nikolaev E, Kostyukevich Y. Investigating the Metabolism of Plants Germinated in Heavy Water, D 2O, and H 218O-Enriched Media Using High-Resolution Mass Spectrometry. Int J Mol Sci 2023; 24:15396. [PMID: 37895078 PMCID: PMC10607710 DOI: 10.3390/ijms242015396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/29/2023] Open
Abstract
Mass spectrometry has been an essential technique for the investigation of the metabolic pathways of living organisms since its appearance at the beginning of the 20th century. Due to its capability to resolve isotopically labeled species, it can be applied together with stable isotope tracers to reveal the transformation of particular biologically relevant molecules. However, low-resolution techniques, which were used for decades, had limited capabilities for untargeted metabolomics, especially when a large number of compounds are labelled simultaneously. Such untargeted studies may provide new information about metabolism and can be performed with high-resolution mass spectrometry. Here, we demonstrate the capabilities of high-resolution mass spectrometry to obtain insights on the metabolism of a model plant, Lepidium sativum, germinated in D2O and H218O-enriched media. In particular, we demonstrated that in vivo labeling with heavy water helps to identify if a compound is being synthesized at a particular stage of germination or if it originates from seed content, and tandem mass spectrometry allows us to highlight the substructures with incorporated isotope labels. Additionally, we found in vivo labeling useful to distinguish between isomeric compounds with identical fragmentation patterns due to the differences in their formation rates that can be compared by the extent of heavy atom incorporation.
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Affiliation(s)
- Sergey Osipenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anton Bashilov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
- Institute for Translational Medicine and Biotechnology, First Moscow State Medical University, 119991 Moscow, Russia
| | - Anna Vishnevskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Lidiia Rumiantseva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anna Levashova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anna Kovalenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Boris Tupertsev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Albert Kireev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
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3
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Kostyukevich Y, Stekolshikova E, Levashova A, Kovalenko A, Vishnevskaya A, Bashilov A, Kireev A, Tupertsev B, Rumiantseva L, Khaitovich P, Osipenko S, Nikolaev E. Untargeted Lipidomics after D 2O Administration Reveals the Turnover Rate of Individual Lipids in Various Organs of Living Organisms. Int J Mol Sci 2023; 24:11725. [PMID: 37511483 PMCID: PMC10380497 DOI: 10.3390/ijms241411725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The administration of low doses of D2O to living organisms was used for decades for the investigation of metabolic pathways and for the measurement of the turnover rate for specific compounds. Usually, the investigation of the deuterium uptake in lipids is performed by measuring the deuteration level of the palmitic acid residue using GC-MS instruments, and to our knowledge, the application of the modern untargeted LC-MS/MS lipidomics approaches was only reported a few times. Here, we investigated the deuterium uptake for >500 lipids for 13 organs and body liquids of mice (brain, lung, heart, liver, kidney, spleen, plasma, urine, etc.) after 4 days of 100% D2O administration. The maximum deuteration level was observed in the liver, plasma, and lung, while in the brain and heart, the deuteration level was lower. Using MS/MS, we demonstrated the incorporation of deuterium in palmitic and stearic fragments in lipids (PC, PE, TAG, PG, etc.) but not in the corresponding free forms. Our results were analyzed based on the metabolic pathways of lipids.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Elena Stekolshikova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Levashova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Scientific Center of Biomedical Technologies of the Federal Medical and Biological Agency, Krasnogorsky District, Village Light Mountains, Bld. 1, 143442 Moscow, Russia
| | - Anna Kovalenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Vishnevskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anton Bashilov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Albert Kireev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Boris Tupertsev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Lidiia Rumiantseva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Sergey Osipenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
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Tupertsev B, Osipenko S, Kireev A, Nikolaev E, Kostyukevich Y. Simple In Vitro 18O Labeling for Improved Mass Spectrometry-Based Drug Metabolites Identification: Deep Drug Metabolism Study. Int J Mol Sci 2023; 24:ijms24054569. [PMID: 36902002 PMCID: PMC10002766 DOI: 10.3390/ijms24054569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
The identification of drug metabolites formed with different in vitro systems by HPLC-MS is a standard step in preclinical research. In vitro systems allow modeling of real metabolic pathways of a drug candidate. Despite the emergence of various software and databases, identification of compounds is still a complex task. Measurement of the accurate mass, correlation of chromatographic retention times and fragmentation spectra are often insufficient for identification of compounds especially in the absence of reference materials. Metabolites can "slip under the nose", since it is often not possible to reliably confirm that a signal belongs to a metabolite and not to other compounds in complex systems. Isotope labeling has proved to be a tool that aids in small molecule identification. The introduction of heavy isotopes is done with isotope exchange reactions or with complicated synthetic schemes. Here, we present an approach based on the biocatalytic insertion of oxygen-18 isotope under the action of liver microsomes enzymes in the presence of 18O2. Using the local anesthetic bupivacaine as an example, more than 20 previously unknown metabolites were reliably discovered and annotated in the absence of the reference materials. In combination with high-resolution mass spectrometry and modern methods of mass spectrometric metabolism data processing, we demonstrated the ability of the proposed approach to increase the degree of confidence in interpretating metabolism data.
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Affiliation(s)
- Boris Tupertsev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
- Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, Institutskiy per., 9, Dolgoprudny, 141701 Moscow, Russia
| | - Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Albert Kireev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center of Molecular and Cellular Biology (CMCB), Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
- Correspondence:
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5
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Kostyukevich Y, Sosnin S, Osipenko S, Kovaleva O, Rumiantseva L, Kireev A, Zherebker A, Fedorov M, Nikolaev EN. PyFragMS-A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways. ACS Omega 2022; 7:9710-9719. [PMID: 35350354 PMCID: PMC8945079 DOI: 10.1021/acsomega.1c07272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS-a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or 16O/18O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.
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Osipenko S, Zherebker A, Rumiantseva L, Kovaleva O, Nikolaev EN, Kostyukevich Y. Oxygen Isotope Exchange Reaction for Untargeted LC-MS Analysis. J Am Soc Mass Spectrom 2022; 33:390-398. [PMID: 35077167 DOI: 10.1021/jasms.1c00383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
LC-MS is a key technique for the identification of small molecules in complex samples. Accurate mass, retention time, and fragmentation spectra from LC-MS experiments are compared to reference values for pure chemical standards. However, this information is often unavailable or insufficient, leading to an assignment to a list of candidates instead of a single hit; therefore, additional features are desired to filter candidates. One such promising feature is the number of specific functional groups of a molecule that can be counted via derivatization or isotope-exchange techniques. Hydrogen/deuterium exchange (HDX) is the most widespread implementation of isotope exchange for mass spectrometry, while oxygen 16O/18O exchange is not applied as frequently as HDX. Nevertheless, it is known that some functional groups may be selectively exchanged in 18O enriched media. Here, we propose an implementation of 16O/18O isotope exchange to highlight various functional groups. We evaluated the possibility of using the number of exchanged oxygen atoms as a descriptor to filter database candidates in untargeted LC-MS-based workflows. It was shown that 16O/18O exchange provides 62% (median, n = 45) search space reduction for a panel of drug molecules. Additionally, it was demonstrated that studying the fragmentation spectra after 16O/18O can aid in eliminating false positives and, in some cases, help to annotate fragments formed with water traces in the collisional cell.
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Affiliation(s)
- Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Alexander Zherebker
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Lidiia Rumiantseva
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Oxana Kovaleva
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Evgeny N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
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Osipenko S, Nikolaev E, Kostyukevich Y. Amine additives for improved in-ESI H/D exchange. Analyst 2022; 147:3180-3185. [DOI: 10.1039/d2an00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-ESI H/D exchange is a convenient technique for analyzing small-molecular complex mixtures.
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Affiliation(s)
- Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
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Zherebker A, Kostyukevich Y, Volkov DS, Chumakov RG, Friederici L, Rüger CP, Kononikhin A, Kharybin O, Korochantsev A, Zimmermann R, Perminova IV, Nikolaev E. Speciation of organosulfur compounds in carbonaceous chondrites. Sci Rep 2021; 11:7410. [PMID: 33795703 PMCID: PMC8016918 DOI: 10.1038/s41598-021-86576-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
Despite broad application of different analytical techniques for studies on organic matter of chondrite meteorites, information about composition and structure of individual compounds is still very limited due to extreme molecular diversity of extraterrestrial organic matter. Here we present the first application of isotopic exchange assisted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis of alkali extractable fraction of insoluble organic matter (IOM) of the Murchison and Allende meteorites. This allowed us to determine the individual S-containing ions with different types of sulfur atoms in IOM. Thiols, thiophenes, sulfoxides, sulfonyls and sulfonates were identified in both samples but with different proportions, which contribution corroborated with the hydrothermal and thermal history of the meteorites. The results were supported by XPS and thermogravimetric analysis coupled to FTICR MS. The latter was applied for the first time for analysis of chondritic IOM. To emphasize the peculiar extraterrestrial origin of IOM we have compared it with coal kerogen, which is characterized by the comparable complexity of molecular composition but its aromatic nature and low oxygen content can be ascribed almost exclusively to degradation of biomacromolecules.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Dmitry S Volkov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Lukas Friederici
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany
| | - Alexey Kononikhin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025.,V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025
| | - Alexander Korochantsev
- Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, Kosygina 19, Moscow, Russia, 119334
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, University of Rostock, 18059, Rostock, Germany.,Joint Mass Spectrometry Centre of Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia, 143025.
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9
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Osipenko S, Botashev K, Nikolaev E, Kostyukevich Y. Transfer learning for small molecule retention predictions. J Chromatogr A 2021; 1644:462119. [PMID: 33845426 DOI: 10.1016/j.chroma.2021.462119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Small molecule retention time prediction is a sophisticated task because of the wide variety of separation techniques resulting in fragmented data available for training machine learning models. Predictions are typically made with traditional machine learning methods such as support vector machine, random forest, or gradient boosting. Another approach is to use large data sets for training with a consequent projection of predictions. Here we evaluate the applicability of transfer learning for small molecule retention prediction as a new approach to deal with small retention data sets. Transfer learning is a state-of-the-art technique for natural language processing (NLP) tasks. We propose using text-based molecular representations (SMILES) widely used in cheminformatics for NLP-like modeling on molecules. We suggest using self-supervised pre-training to capture relevant features from a large corpus of one million molecules followed by fine-tuning on task-specific data. Mean absolute error (MAE) of predictions was in range of 88-248 s for tested reversed-phase data sets and 66 s for HILIC data set, which is comparable with MAE reported for traditional machine learning models based on descriptors or projection approaches on the same data.
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Affiliation(s)
- Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Kazii Botashev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia.
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia.
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Sarycheva A, Grigoryev A, Sidorchuk D, Vladimirov G, Khaitovich P, Efimova O, Gavrilenko O, Stekolshchikova E, Nikolaev EN, Kostyukevich Y. Structure-Preserving and Perceptually Consistent Approach for Visualization of Mass Spectrometry Imaging Datasets. Anal Chem 2021; 93:1677-1685. [PMID: 33373190 DOI: 10.1021/acs.analchem.0c04256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry imaging (MSI) has become an important tool for 2D profiling of biological tissues, allowing for the visualization of individual compound distributions in the sample. Based on this information, it is possible to investigate the molecular organization within any particular tissue and detect abnormal regions (such as tumor regions) and many other biologically relevant phenomena. However, the large number of compounds present in the spectra hinders the productive analysis of large MSI datasets when utilizing standard tools. The heterogeneity of samples makes exploratory visualization (a presentation of the general idea of the molecular and structural organization of the inspected tissues) challenging. Here, we explore the application of various dimensionality reduction techniques that have been used extensively in the visualization of hyperspectral images and the MSI data specifically, such as principal component analysis, independent component analysis, non-negative matrix factorization, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. Further, we propose a new approach based on a combination of structure preserving visualization with nonlinear manifold embedding of normalized spectral data. This way, we aim to preserve as much spatially overlapping signals as possible while augmenting them with information on compositional (spectral) variation. The proposed approach can be used for exploratory visualization of MSI datasets without prior deep chemical or histological knowledge of the sample. Thus, different datasets can be visually compared employing the proposed method. The proposed approach allowed for the clear visualization of the molecular layer, granular layer, and white matter in chimpanzee and macaque cerebellum slices.
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Affiliation(s)
- Anastasia Sarycheva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Anton Grigoryev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russian Federation
| | - Dmitry Sidorchuk
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russian Federation
| | - Gleb Vladimirov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Olga Gavrilenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Elena Stekolshchikova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow 121205, Russian Federation
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11
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Fedorov FS, Yaqin A, Krasnikov DV, Kondrashov VA, Ovchinnikov G, Kostyukevich Y, Osipenko S, Nasibulin AG. Detecting cooking state of grilled chicken by electronic nose and computer vision techniques. Food Chem 2020; 345:128747. [PMID: 33307429 DOI: 10.1016/j.foodchem.2020.128747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 01/26/2023]
Abstract
Determination of food doneness remains a challenge for automation in the cooking industry. The complex physicochemical processes that occur during cooking require a combination of several methods for their control. Herein, we utilized an electronic nose and computer vision to check the cooking state of grilled chicken. Thermogravimetry, differential mobility analysis, and mass spectrometry were employed to deepen the fundamental insights towards the grilling process. The results indicated that an electronic nose could distinguish the odor profile of the grilled chicken, whereas computer vision could identify discoloration of the chicken. The integration of these two methods yields greater selectivity towards the qualitative determination of chicken doneness. The odor profile is matched with detected water loss, and the release of aromatic and sulfur-containing compounds during cooking. This work demonstrates the practicability of the developed technique, which we compared with a sensory evaluation, for better deconvolution of food state during cooking.
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Affiliation(s)
- Fedor S Fedorov
- Laboratory of Nanomaterials, Skolkovo Institute of Science and Technology, 3 Nobel St., 121205 Moscow, Russia.
| | - Ainul Yaqin
- Laboratory of Nanomaterials, Skolkovo Institute of Science and Technology, 3 Nobel St., 121205 Moscow, Russia.
| | - Dmitry V Krasnikov
- Laboratory of Nanomaterials, Skolkovo Institute of Science and Technology, 3 Nobel St., 121205 Moscow, Russia.
| | - Vladislav A Kondrashov
- Laboratory of Nanomaterials, Skolkovo Institute of Science and Technology, 3 Nobel St., 121205 Moscow, Russia.
| | - George Ovchinnikov
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, 3 Nobel Str., 121205 Moscow, Russia.
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, 3 Nobel Str., 121205 Moscow, Russia.
| | - Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, 3 Nobel Str., 121205 Moscow, Russia.
| | - Albert G Nasibulin
- Laboratory of Nanomaterials, Skolkovo Institute of Science and Technology, 3 Nobel St., 121205 Moscow, Russia; Aalto University, 00076 Espoo, Finland.
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12
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Zherebker A, Lechtenfeld OJ, Sarycheva A, Kostyukevich Y, Kharybin O, Fedoros EI, Nikolaev EN. Refinement of Compound Aromaticity in Complex Organic Mixtures by Stable Isotope Label Assisted Ultrahigh-Resolution Mass Spectrometry. Anal Chem 2020; 92:9032-9038. [PMID: 32484343 DOI: 10.1021/acs.analchem.0c01208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a unique opportunity for molecular analysis of natural complex mixtures. In many geochemical and environmental studies structure-propertry relations are based solely on the elemental compositional information. Several calculated parameters were proposed to increase reliability of structural attribution, among which aromaticity indices (AI and AImod) are widely used. Herein, we applied a combination of selective labeling reactions in order to obtain direct structural information on the individual components of lignin-derived polyphenolic material. Carboxylic (COOH), carbonyl (C═O), and hydroxyl (OH) groups were enumerated by esterification, reducing, and acetylation reactions, respectively, followed by FTICR MS analyses. Obtained information was enabled to constrain aromaticity accounting for the carbon skeleton only. We found that actual aromaticity of components may be both higher or lower than approximated values depending on the abundance of COOH, C═O, and OH groups. The results are of importance for the geochemical community studying terrestrial NOM with structural gradients.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig DE-04318, Germany
| | - Anastasia Sarycheva
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia.,Nobel LTD, Saint-Petersburg 192012, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
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13
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Kostyukevich Y, Zherebker A, Orlov A, Kovaleva O, Burykina T, Isotov B, Nikolaev EN. Hydrogen/Deuterium and 16O/ 18O-Exchange Mass Spectrometry Boosting the Reliability of Compound Identification. Anal Chem 2020; 92:6877-6885. [PMID: 32167749 DOI: 10.1021/acs.analchem.9b05379] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate and reliable identification of chemical compounds is the ultimate goal of mass spectrometry analyses. Currently, identification of compounds is usually based on the measurement of the accurate mass and fragmentation spectrum, chromatographic elution time, and collisional cross section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud and Metlin) and developing software for predicting MS/MS fragments in silico from SMILES patterns (such as MetFrag, CFM-ID, and Ms-Finder), the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of big help for LC-MS/MS-based omics. Our approach is based on the characterization of compounds by the number of labile hydrogen and oxygen atoms in the molecule, which can be measured using hydrogen/deuterium and 16O/18O-exchange approaches. The number of labile atoms (those from -OH, -NH, ═O, and -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing a database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here, we present an approach utilizing the selection of structural candidates from a database on the basis of the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reduction of the search space by a factor of 10 and considerably increases the reliability of the compound identification.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexey Orlov
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Oxana Kovaleva
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Tatyana Burykina
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Boris Isotov
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
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14
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Kostyukevich Y, Vladimirov G, Stekolschikova E, Ivanov D, Yablokov A, Zherebker A, Sosnin S, Orlov A, Fedorov M, Khaitovich P, Nikolaev E. Hydrogen/Deuterium Exchange Aiding Compound Identification for LC-MS and MALDI Imaging Lipidomics. Anal Chem 2019; 91:13465-13474. [PMID: 31490663 DOI: 10.1021/acs.analchem.9b02461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We present a novel approach for the increasing reliability of compound identification for LC-MS and MALDI imaging lipidomics. Our approach is based on the characterization of compounds not only by the elution time, accurate mass, and fragmentation spectra but also by the number of labile hydrogens that can be measured using the hydrogen/deuterium (H/D) exchange approach. The number of labile hydrogens (those from -OH and -NH groups) serves as an additional structural descriptor used when performing a database search. For LC-MS experiment, the H/D exchange was performed in the heating capillary of the modified electrospray ionization (ESI) source, while for MALDI imaging, the exchange was performed in the ion funnel at 10 Torr pressure. It was observed that such an approach allowed one to achieve a considerable degree of deuteration, enough to unambiguously distinguish between different classes of lipids. The proposed analytical approach may be successfully used for the identification not only of lipids but also of peptides and metabolites. A special software for the automatic filtration of molecules based on the number of functional groups was also developed.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation.,Moscow Institute of Physics and Technology , Dolgoprudnyi , Moscow Region 141700 , Russia
| | - Gleb Vladimirov
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Elena Stekolschikova
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Daniil Ivanov
- Moscow Institute of Physics and Technology , Dolgoprudnyi , Moscow Region 141700 , Russia.,Emanuel Institute of Biochemical Physics , Russian Academy of Sciences , Kosygina Street, 4 , Moscow 119334 , Russia
| | - Arthur Yablokov
- Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninskij pr. 38 k.2 , Moscow 119334 , Russia
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Sergey Sosnin
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Alexey Orlov
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Maxim Fedorov
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
| | - Evgeny Nikolaev
- Skolkovo Institute of Science and Technology , Novaya Street, 100 , Skolkovo 143025 , Russian Federation
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15
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Orlov AA, Zherebker A, Eletskaya AA, Chernikov VS, Kozlovskaya LI, Zhernov YV, Kostyukevich Y, Palyulin VA, Nikolaev EN, Osolodkin DI, Perminova IV. Examination of molecular space and feasible structures of bioactive components of humic substances by FTICR MS data mining in ChEMBL database. Sci Rep 2019; 9:12066. [PMID: 31427609 PMCID: PMC6700089 DOI: 10.1038/s41598-019-48000-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 07/29/2019] [Indexed: 01/08/2023] Open
Abstract
Humic substances (HS) are complex natural mixtures comprising a large variety of compounds produced during decomposition of decaying biomass. The molecular composition of HS is extremely diverse as it was demonstrated with the use of high resolution mass spectrometry. The building blocks of HS are mostly represented by plant-derived biomolecules (lignins, lipids, tannins, carbohydrates, etc.). As a result, HS show a wide spectrum of biological activity. Despite that, HS remain a 'biological activity black-box' due to unknown structures of constituents responsible for the interaction with molecular targets. In this study, we investigated the antiviral activity of eight HS fractions isolated from peat and coal, as well as of two synthetic humic-like materials. We determined molecular compositions of the corresponding samples using ultra-high resolution Fourier-transform ion cyclotron resonance mass-spectrometry (FTICR MS). Inhibitory activity of HS was studied with respect to reproduction of tick-borne encephalitis virus (TBEV), which is a representative of Flavivirus genus, and to a panel of enteroviruses (EVs). The samples of natural HS inhibited TBEV reproduction already at a concentration of 1 µg/mL, but they did not inhibit reproduction of EVs. We found that the total relative intensity of FTICR MS formulae within elemental composition range commonly attributed to flavonoid-like structures is correlating with the activity of the samples. In order to surmise on possible active structural components of HS, we mined formulae within FTICR MS assignments in the ChEMBL database. Out of 6502 formulae within FTICR MS assignments, 3852 were found in ChEMBL. There were more than 71 thousand compounds related to these formulae in ChEMBL. To support chemical relevance of these compounds to natural HS we applied the previously developed approach of selective isotopic exchange coupled to FTICR MS to obtain structural information on the individual components of HS. This enabled to propose compounds from ChEMBL, which corroborated the labeling data. The obtained results provide the first insight onto the possible structures, which comprise antiviral components of HS and, respectively, can be used for further disclosure of antiviral activity mechanism of HS.
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Affiliation(s)
- Alexey A Orlov
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anastasia A Eletskaya
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Department of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Liubov I Kozlovskaya
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Yury V Zhernov
- State Research Center "Institute of Immunology" of the Federal Medical-Biological Agency of Russia, Moscow, 115478, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Dmitry I Osolodkin
- FSBSI "Chumakov FSC R&D IBP RAS", Moscow, 108819, Russia.
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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16
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Zherebker A, Perminova IV, Kostyukevich Y, Kononikhin AS, Kharybin O, Nikolaev E. Structural investigation of coal humic substances by selective isotopic exchange and high-resolution mass spectrometry. Faraday Discuss 2019; 218:172-190. [PMID: 31115412 DOI: 10.1039/c9fd00002j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here, we report the application of a selective liquid-phase hydrogen/deuterium exchange (HDX) coupled to ultra-high resolution FTICR MS for structural investigations of individual constituents of humic substances (HS) isolated from three coal samples of different geographical origin. Selectivity was achieved by conducting reactions in DCl or NaOD solutions for catalyzing HDX in aromatic ring and side-chain positions with enhanced C-H acidity, respectively. FTICR MS analysis showed a significant overlap of molecular compositions in the HS samples under study, with 2000 common formulae. Using HDX, we demonstrated that the determined common formulae are presented by different structural isomers. We found that aromatic compounds varied both in the substitution pattern and the number of aromatic protons. Depending on the sample, lignin components with the same molecular formulae were composed of coumaryl, coniferyl or sinapyl moieties. Enumeration of HDX series for the 800 most abundant compounds showed that the results of HDX agreed well with the model structures suggested for humic components occupying a van Krevelen plot. In addition, we explored chemical transformations, which could connect individual constituents of coal HS. These transformations included hydrolysis of a guaiacyl moiety and reduction of a catechol unit, which corresponds to the conversion of a coniferyl fragment into a coumaryl unit. The obtained results were supportive of the hypothesis of the reducing humification pathway suggested for lignin transformation in the environment. The conclusion was made that the molecular ensemble of coal HS is composed of individual constituents produced at different humification stages.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia.
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17
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Kostyukevich Y, Kitova A, Zherebker A, Rukh S, Nikolaev E. Investigation of the archeological remains using ultrahigh resolution mass spectrometry. Eur J Mass Spectrom (Chichester) 2019; 25:391-396. [PMID: 30939934 DOI: 10.1177/1469066719840287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Investigation of the archeological material at the molecular level can reveal the composition of ancient paint, balsamic material, reveal cooking recipes, etc. High-resolution mass spectrometry is a powerful technique with underestimated potential for archeology. Here, we present the investigation of the 3000-year-old archeological remains, identified as parts of internal organs of an Egyptian mummy, using high-resolution Orbitrap mass spectrometry. We observed a diverse number of oxidized classes of compounds: O, O2, O3, O4, O5, N, NO, NO2, NO3, NO4, NO5, N2O, N2O2. Such chemical composition is unusual and we never observed it in our previous studies of petroleum, humic substances, products of wood pyrolysis or other natural complex mixtures. It is possible that such compounds are formed via biodegradation of lipids and other organic material used for funeral rites. We did not observe evidence of the presence of mineral bitumen, although there are many historical records of the use of mineral bitumen for mummification.
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Affiliation(s)
- Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Alexandra Kitova
- 3 Center for Egyptological Studies of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zherebker
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Shah Rukh
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
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18
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Kostyukevich Y, Vlaskin M, Zherebker A, Grigorenko A, Borisova L, Nikolaev E. High-Resolution Mass Spectrometry Study of the Bio-Oil Samples Produced by Thermal Liquefaction of Microalgae in Different Solvents. J Am Soc Mass Spectrom 2019; 30:605-614. [PMID: 30761476 DOI: 10.1007/s13361-018-02128-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
We have performed a comparative analysis of the bio-oil produced by thermal liquefaction of microalgae in different solvents using high-resolution Orbitrap mass spectrometry and GC-MS approach. Water, methanol, ethanol, butanol, isopropanol, acetonitrile, toluene, and hexane were used as solvents in which the liquefaction was performed. It was observed that all resulting oils demonstrate a considerable degree of similarity. For all samples, compounds containing 1 and 2 nitrogen atoms dominated in the positive ESI spectra, while a relative contribution of other compounds was small. In negative ESI mode, compounds having 2 to 7 oxygens were observed. Statistical analysis revealed that products can be combined in two groups depending on the solvent used for the liquefaction. To the first group, we can attribute the products obtained by using protic (alcohols) and to the second by using aprotic (acetonitrile, toluene) solvents. Nevertheless, based on our results, we concluded that solvent possesses a minor impact on molecular composition of bio-oil. We suggested that the driving force of the liquefaction reaction is the thermal dehydration of the carbohydrate in algae, resulting in water formation, which could be the trigger of the producing of bio-oil. To prove this hypothesis, we performed the reaction with the dry algae in the absence of the solvent and observed the formation of bio-oil. Graphical Abstract.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St. 100, Skolkovo, Moscow, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, 141700, Russia
| | - Mihail Vlaskin
- Joint Institute for High Temperatures (JIHT) of Russian Academy of Sciences, Izhorskaya st. 13 Bd.2, Moscow, 125412, Russia
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Novaya St. 100, Skolkovo, Moscow, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia
| | - Anatoly Grigorenko
- Joint Institute for High Temperatures (JIHT) of Russian Academy of Sciences, Izhorskaya st. 13 Bd.2, Moscow, 125412, Russia
| | - Ludmila Borisova
- National Research University Higher School of Economics, 20 Miasnitskaya Ulitsa, Moscow, 101000, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St. 100, Skolkovo, Moscow, 143025, Russia.
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, 141700, Russia.
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19
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Chagovets V, Kononikhin A, Tokoreva A, Bormotov D, Starodubtseva N, Kostyukevich Y, Popov I, Frankevich V, Nikolaev E. Relative quantitation of phosphatidylcholines with interfered masses of protonated and sodiated molecules by tandem and Fourier-transform ion cyclotron resonance mass spectrometry. Eur J Mass Spectrom (Chichester) 2019; 25:259-264. [PMID: 31018698 DOI: 10.1177/1469066718799992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The present work deals with deconvolution of interfered peaks of protonated and sodiated phosphatidylcholines to solve the problem of relative quantitation of these compounds. The method was developed based on the fact that adducts of phosphatidylcholines with proton and sodium ion give unique characteristic peaks in tandem mass spectrometry. Ultra-high-resolution Fourier-transform ion cyclotron resonance mass spectrometry was used to resolve interfered peaks and thus validate the results of tandem mass spectrometry-based deconvolution. Applicability of the method was tested with synthesized phosphatidylcholines and applied for tissue-spray analysis of the clinical samples and demonstrated good correlation (0.996) between MS/MS and Fourier-transform ion cyclotron resonance mass spectrometry results.
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Affiliation(s)
- Vitaliy Chagovets
- 1 V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Aleksey Kononikhin
- 1 V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
- 2 V. L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alisa Tokoreva
- 2 V. L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Denis Bormotov
- 2 V. L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Nataliia Starodubtseva
- 1 V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Yury Kostyukevich
- 4 N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
| | - Igor Popov
- 1 V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Vladimir Frankevich
- 1 V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Eugene Nikolaev
- 2 V. L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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20
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Zakalyukina YV, Birykov MV, Lukianov DA, Shiriaev DI, Komarova ES, Skvortsov DA, Kostyukevich Y, Tashlitsky VN, Polshakov VI, Nikolaev E, Sergiev PV, Osterman IA. Nybomycin-producing Streptomyces isolated from carpenter ant Camponotus vagus. Biochimie 2019; 160:93-99. [PMID: 30797881 DOI: 10.1016/j.biochi.2019.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/18/2019] [Indexed: 11/17/2022]
Abstract
A novel strain of Actinomycetes was isolated from the body of an ant (Camponotus vagus Scopoli) and its genetic and morphological properties were characterized. The 16S rDNA gene sequence analysis of the isolate revealed its high phylogenetic relationship with type strains of Streptomyces violaceochromogenes NBRC 13100T. As a result of antimicrobial activity assessment, it was found that the fermentation broth of the isolated strain both inhibited the growth and induced the SOS response in E. coli BW25113 ΔtolC strain cells. Using bioassay-guided fractionation, mass spectrometric and NMR analyses we identified the active compound to be nybomycin, a previously described antibiotic. Here we report for the first time Streptomyces producer of nybomycin in association with carpenter ants and demonstrate cytotoxic activity of nybomycin against human cell lines.
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Affiliation(s)
- Yuliya V Zakalyukina
- Department of Soil Science, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Mikhail V Birykov
- Department of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Dmitrii A Lukianov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia
| | - Dmitrii I Shiriaev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ekaterina S Komarova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Dmitry A Skvortsov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V., Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia
| | - Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia; Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ilya A Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia; Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
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Gridnev ID, Zherebker A, Kostyukevich Y, Nikolaev E. Methylene Group Transfer in Carbonyl Compounds Discovered in silico and Detected Experimentally. Chemphyschem 2019; 20:361-365. [PMID: 30523648 DOI: 10.1002/cphc.201800945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/04/2018] [Indexed: 11/10/2022]
Abstract
A previously unknown transformation of aldehydes, ketones, and carboxylic acid derivatives leads to the formation of substituted oxiranes, aziridines, and azirines as shown by DFT and MP2 computations. Formations of 2,2-dimethyloxirane-d8 from acetone-d6 , phenylazirine-d2 from benzonitrile and 2-methyl-2-(4-hydroxyphenyl)-oxirane from 4-hydroxyacetophenone were detected experimentally by electrospray ionization mass-spectrometry with a heated desolvating capillary. This reaction is a truly concerted process characterized by high activation barriers (activation enthalpies 320-480 kJ mol-1 ).
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Affiliation(s)
- Ilya D Gridnev
- Graduate School of Science, Tohoku University Aramaki Aza Aoba 6-3, Aoba-ku, Sendai, 9808578, Japan
| | - Alexander Zherebker
- Center of Life Science, Skolkovo institute of Science and technology, 3 Nobelya str., Moscow, 121205, Russia
| | - Yury Kostyukevich
- Center of Life Science, Skolkovo institute of Science and technology, 3 Nobelya str., Moscow, 121205, Russia
| | - Eugene Nikolaev
- Center of Life Science, Skolkovo institute of Science and technology, 3 Nobelya str., Moscow, 121205, Russia
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22
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Zherebker A, Shirshin E, Kharybin O, Kostyukevich Y, Kononikhin A, Konstantinov AI, Volkov D, Roznyatovsky VA, Grishin YK, Perminova IV, Nikolaev E. Separation of Benzoic and Unconjugated Acidic Components of Leonardite Humic Material Using Sequential Solid-Phase Extraction at Different pH Values as Revealed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Correlation Nuclear Magnetic Resonance Spectroscopy. J Agric Food Chem 2018; 66:12179-12187. [PMID: 30335379 DOI: 10.1021/acs.jafc.8b04079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we report on sequential solid-phase extraction of leonardite hymatomelanic acid (CHM) on a non-ionic sorbent at four steadily lowered pH values: 7, 5, 3, and 2, yielding fractions with different acidic properties. Using nuclear magnetic resonance (NMR) spectroscopy and ultrahigh-resolution mass spectrometry, we revealed a gradual shift of dominating scaffolds in the fractions of CHM from reduced saturated to oxidized aromatic compounds. An increase on the average aromaticity of the CHM fractions was accompanied by a red shift in fluorescence spectra. These results were supported by heteronuclear single quantum coherence and heteronuclear multiple bond correlation NMR experiments. We have demonstrated that the CHM fraction isolated at pH 5 was dominated by aliphatic carboxyl carriers, while the pH 3 fraction was dominated by aromatic carboxyl acids. The developed fractionation technique will enable deeper insight on structure-property relationships and the design of the humic-based materials with tailored reactive properties.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
| | - Evgeny Shirshin
- Department of Physics , Lomonosov Moscow State University , Leninskie Gory 1/2 , 119991 Moscow , Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Orekhovich Institute of Biomedical Chemistry , Russian Academy of Sciences , Pogodinskaya Ulitsa 10 , 119121 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
| | - Andrey I Konstantinov
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Dmitry Volkov
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | | | - Yuri K Grishin
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Irina V Perminova
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology , 143025 Skolkovo , Moscow Region, Russia
- Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences , Leninskij Prospekt 38-2 , 119334 Moscow , Russia
- Orekhovich Institute of Biomedical Chemistry , Russian Academy of Sciences , Pogodinskaya Ulitsa 10 , 119121 Moscow , Russia
- Moscow Institute of Physics and Technology , 141700 Dolgoprudnyi , Moscow Region, Russia
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23
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Kostyukevich Y, Acter T, Zherebker A, Ahmed A, Kim S, Nikolaev E. Hydrogen/deuterium exchange in mass spectrometry. Mass Spectrom Rev 2018; 37:811-853. [PMID: 29603316 DOI: 10.1002/mas.21565] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 05/22/2023]
Abstract
The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | - Thamina Acter
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Republic of Korea
- Green Nano Center, Kyungpook National University, Daegu, Republic of Korea
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
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24
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Kostyukevich Y, Zherebker A, Vlaskin MS, Borisova L, Nikolaev E. Microprobe for the Thermal Analysis of Crude Oil Coupled to Photoionization Fourier Transform Mass Spectrometry. Anal Chem 2018; 90:8756-8763. [DOI: 10.1021/acs.analchem.8b02043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya Street, 100, Skolkovo 143025, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology, Novaya Street, 100, Skolkovo 143025, Russia
| | | | - Ludmila Borisova
- National Research University Higher School of Economics, 20 Miasnitskaya Ulitsa, Moscow 101000, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street, 100, Skolkovo 143025, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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25
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo 143025, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo 143025, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
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26
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya Street, 100, Skolkovo 143025, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij prospekt 38 k.2, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya Street, 100, Skolkovo 143025, Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij prospekt 38 k.2, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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27
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Kostyukevich Y, Vlaskin M, Borisova L, Zherebker A, Perminova I, Kononikhin A, Popov I, Nikolaev E. Investigation of bio-oil produced by hydrothermal liquefaction of food waste using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry. Eur J Mass Spectrom (Chichester) 2018; 24:116-123. [PMID: 29050496 DOI: 10.1177/1469066717737904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent research has revealed that more than 1.3 billion tons of food is wasted globally every year. The disposal of such huge biomass has become a challenge. In the present paper, we report the production of the bio-oil by hydrothermal liquefaction of three classes of food waste: meat, cheese and fruits. The highest yield of the bio-oil was observed for meat (∼60%) and cheese (∼75%), while for fruits, it was considerably low (∼10%). The molecular composition of the obtained bio-oil was investigated using ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry and was found to be similar to that obtained from algae. Several thousand heteroatom compounds (N, N2, ON2, etc. classes) were reliably identified from each sample. It was found that bio-oils produced from meat and cheese have many compounds (∼90%) with common molecular formulas, while bio-oil produced from fruits differs considerably (∼30% of compounds are unique).
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Affiliation(s)
- Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 4 The Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Vlaskin
- 4 The Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia
| | - Ludmila Borisova
- 5 National Research University Higher School of Economics, Moscow, Russia
| | - Alexander Zherebker
- 6 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Irina Perminova
- 6 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Kononikhin
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 The Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia
| | - Igor Popov
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Moscow Institute of Physics and Technology, Moscow Region, Russia
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28
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Kostyukevich Y, Efremov D, Ionov V, Kukaev E, Nikolaev E. Remote detection of explosives using field asymmetric ion mobility spectrometer installed on multicopter. J Mass Spectrom 2017; 52:777-782. [PMID: 28762581 DOI: 10.1002/jms.3980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
The detection of explosives and drugs in hard-to-reach places is a considerable challenge. We report the development and initial experimental characterization of the air analysis system that includes Field Asymmetric Ion Mobility Spectrometer, array of the semiconductor gas sensors and is installed on multicopter. The system was developed based on the commercially available DJI Matrix 100 platform. For data collection and communication with operator, the special compact computer (Intel Compute Stick) was installed onboard. The total weight of the system was 3.3 kg. The system allows the 15-minute flight and provides the remote access to the obtained data. The developed system can be effectively used for the detection of impurities in the air, ecology monitoring, detection of chemical warfare agents, and explosives, what is especially important in light of recent terroristic attacks. The capabilities of the system were tested on the several explosives such as trinitrotoluene and nitro powder.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, 143025, Skolkovo, Russia
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences, Kosygina St. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow, Russia
| | - Denis Efremov
- Private educational institution of higher professional education Moscow Technological Institute, Leninsky Prospect 38a, 119334, Moscow, Russia
| | - Vladimir Ionov
- "Lavanda-U Limited" 111123, Shosse Entuziastov, d. 56, p. 27, Moscow, Russia
| | - Eugene Kukaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, 143025, Skolkovo, Russia
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences, Kosygina St. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow, Russia
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29
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Kostyukevich Y, Stavitskaya A, Zherebker A, Konstantinova M, Vlaskin M, Borisova L, Kononikhin A, Popov I, Nikolaev E. Investigation of the ozonation products of natural complex mixtures using Fourier transform ion cyclotron resonance mass spectrometry. Eur J Mass Spectrom (Chichester) 2017; 23:152-155. [PMID: 29028389 DOI: 10.1177/1469066717718836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Natural complex mixtures such as oil and dissolved organic matter play an important role in the economy and in the global carbon cycle. One of the most promising approaches for the investigation of the chemical structure of such substances is the combination of the high-resolution mass spectrometry and selective chemical reactions. Here, we report the investigation of the ozonation products of natural complex mixtures using Fourier transform ion cyclotron resonance mass spectrometry. Ozonation of crude oil results in the appearance of the new compounds with high content (up to 9 atom) of oxygen. Isotopic exchange reaction showed that those oxygen stem from the carbonyl groups. Ozonation of the dissolved organic matter leads to the destruction of the substance and shift towards the region of the saturated compounds.
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Affiliation(s)
- Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics Russia Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics Russia Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
- 5 The Joint Institute for High Temperatures of Russia Academy of Sciences, Moscow, Russia
| | | | - Alexander Zherebker
- 1 Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics Russia Academy of Sciences, Moscow, Russia
- 7 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Konstantinova
- 3 Emanuel Institute for Biochemical Physics Russia Academy of Sciences, Moscow, Russia
| | - Mikhail Vlaskin
- 5 The Joint Institute for High Temperatures of Russia Academy of Sciences, Moscow, Russia
| | - Ludmila Borisova
- 8 National Research University Higher School of Economics, Moscow, Russia
| | - Alexey Kononikhin
- 2 Institute for Energy Problems of Chemical Physics Russia Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Igor Popov
- 3 Emanuel Institute for Biochemical Physics Russia Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics Russia Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics Russia Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
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Vladimirov G, Kostyukevich Y, Kharybin O, Nikolaev E. Effect of ion clouds micromotion on measured signal in Fourier transform ion cyclotron resonance: Computer simulation. Eur J Mass Spectrom (Chichester) 2017; 23:162-166. [PMID: 29028402 DOI: 10.1177/1469066717718837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Particle-in-cell-based realistic simulation of Fourier transform ion cyclotron resonance experiments could be used to generate ion trajectories and a signal induced on the detection electrodes. It has been shown recently that there is a modulation of "reduced" cyclotron frequencies in ion cyclotron resonance signal caused by Coulomb interaction of ion clouds. In this work it was proposed to use this modulation in order to determine frequency difference between an ion of known m/z and all other ions generating signal in ion cyclotron resonance cell. It is shown that with an increase of number of ions in ion cyclotron resonance trap, the modulation index increases, which lead to a decrease in the accuracy of determination of peak intensities by super Fourier transform resolution methods such as filter diagonalization method.
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Affiliation(s)
- Gleb Vladimirov
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Oleg Kharybin
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
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Sorokin A, Zhvansky E, Shurkhay V, Bocharov K, Popov I, Levin N, Zubtsov D, Bormotov D, Kostyukevich Y, Potapov A, Nikolaev E. Feature selection algorithm for spray-from-tissue mass spectrometry. Eur J Mass Spectrom (Chichester) 2017; 23:237-241. [PMID: 29028388 DOI: 10.1177/1469066717721843] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Detection of the brain tumor margins is one of the most significant problems in neurosurgery. Several mass spectrometry-based approaches have been proposed recently for tumor boundary detection. One of them, spray from tissue does not require sample preparation but needs special algorithms for analysis of its spectra. Here we proposed the feature selection algorithm designed for analysis of spray-from-tissue data.
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Affiliation(s)
- Anatoly Sorokin
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Evgeny Zhvansky
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russia
| | - Vsevolod Shurkhay
- 3 Federal State Autonomous Institution "N.N. Burdenko National Scientific and Practical Center for Neurosurgery" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Konstantin Bocharov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russia
| | - Igor Popov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- 4 Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia
| | - Nikita Levin
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Dmitry Zubtsov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Denis Bormotov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Yury Kostyukevich
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Potapov
- 3 Federal State Autonomous Institution "N.N. Burdenko National Scientific and Practical Center for Neurosurgery" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Eugene Nikolaev
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russia
- 4 Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia
- 5 Skolkovo Institute of Science and Technology, Skolkovo, Russia
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32
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Zhdanova E, Kostyukevich Y, Nikolaev E. Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell. Eur J Mass Spectrom (Chichester) 2017; 23:197-201. [PMID: 29028404 DOI: 10.1177/1469066717718369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Static harmonization in the Fourier transform ion cyclotron resonance cell improves the resolving power of the cell and prevents dephasing of the ion cloud in the case of any trajectory of the charged particle, not necessarily axisymmetric cyclotron (as opposed to dynamic harmonization). We reveal that the Fourier transform ion cyclotron resonance cell with dynamic harmonization (paracell) is proved to be statically harmonized. The volume of the statically harmonized potential distribution increases with an increase in the number of trap segments.
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Affiliation(s)
- Ekaterina Zhdanova
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Yury Kostyukevich
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Eugene Nikolaev
- 1 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow Region, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Zherebker A, Turkova AV, Kostyukevich Y, Kononikhin A, Zaitsev KV, Popov IA, Nikolaev E, Perminova IV. Synthesis of carboxylated styrene polymer for internal calibration of Fourier transform ion cyclotron resonance mass-spectrometry of humic substances. Eur J Mass Spectrom (Chichester) 2017; 23:156-161. [PMID: 29028407 DOI: 10.1177/1469066717718963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report synthesis and application of the novel carboxylated styrene for internal calibration of Fourier transform ion cyclotron resonance mass-spectra of humic substances. The calibrant was synthesized in five steps from acetylsalicylic acid (aspirin) followed by spontaneous polymerization of vinyl salicylic acid. Aromatic nature of the prepared polymer enabled its simultaneous analysis in the presence of the Suwannee River fulvic acid without using dual-spray approach. The major advantage of the calibrant proposed in this study is a lack of suppression of humic substances signals and maintenance of peak intensity distribution. The appropriate calibration resulted in an increased number of unambiguous identification in Suwannee River fulvic acid. Thanks to the higher mass accuracy, it was also possible to refine attribution of the CHOS species to hydrolysable tannins as opposed to the erroneous previous assignment to the condensed tannins.
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Affiliation(s)
- Alexander Zherebker
- 1 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra V Turkova
- 1 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yury Kostyukevich
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 4 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Kononikhin
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Kirill V Zaitsev
- 1 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Igor A Popov
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Eugene Nikolaev
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Skolkovo Institute of Science and Technology, Skolkovo, Russia
- 4 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Irina V Perminova
- 1 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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Kostyukevich Y, Shulga AA, Kononikhin A, Popov I, Nikolaev E, Deyev S. CID fragmentation, H/D exchange and supermetallization of Barnase-Barstar complex. Sci Rep 2017; 7:6176. [PMID: 28733680 PMCID: PMC5522418 DOI: 10.1038/s41598-017-06507-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/13/2017] [Indexed: 01/02/2023] Open
Abstract
The barnase-barstar complex is one of the most stable protein-protein complexes and has a very wide range of possible applications. Here we report the use of top-down mass spectrometry for the investigation of the structure of this complex, its ionization via ESI, isolation and fragmentation. It was found that the asymmetry of the resulting charge state distributions of the protein monomer product ions increased as the charge state of the precursor ions increased. For the investigation of the 3D structure of the complex, the gas phase H/D exchange reaction was used. In addition, supermetallized ions of the complex with Zn were produced and investigated. It was observed that an increase in the number of metals bound to the complex results in a change in complex stability and the charge distribution between protein fragment. Analysis of the fragmentation pattern of the supermetallized complex [bn-b* + 5Zn]10+ indicated that this ion is present in different conformations with different charges and Zn distributions. Since Zn cannot migrate, such structures must be formed during ionization.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo, 143025, Russian Federation.,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia.,Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Aleksej A Shulga
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya str., Moscow, 117997, Russian Federation
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo, 143025, Russian Federation. .,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38, k.2, 119334, Moscow, Russia. .,Emanuel Institute for Biochemical Physics, Russian Academy of Sciences Kosygina st. 4, 119334, Moscow, Russia. .,Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia.
| | - Sergey Deyev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10, Miklukho-Maklaya str., Moscow, 117997, Russian Federation.,National Research Tomsk Polytechnic University, 30, av. Lenina, Tomsk, 634050, Russia
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Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. Thermal dissociation of ions limits the degree of the gas-phase H/D exchange at the atmospheric pressure. J Mass Spectrom 2017; 52:204-209. [PMID: 28152260 DOI: 10.1002/jms.3917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
We present the application of the extended desolvating capillaries for increasing the degree of the gas-phase hydrogen/deuterium exchange reaction at atmospheric pressure. The use of the extended capillaries results in the increase of the time that ions spend in the high pressure region, what leads to the significant improvement of the efficiency of the reaction. For the small protein ubiquitin, it was observed that for the same temperature, the number of exchanges increases with the decrease of the charge state so that the lowest charge state can exchange twice the number of hydrogen than the highest one. With the increase of the temperature, the difference decreases, and eventually, the number of exchanges equalizes for all charge states. The value of this temperature and the corresponding number of exchanges depend on the geometric parameters of the capillary. Further increase of the temperature leads to the thermal dissociation of the protein ion. The observed b/y fragments are identical to those produced by collision-induced dissociation performed in the ion trap. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Y Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - A Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - I Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - E Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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36
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Kostyukevich Y, Vlaskin M, Vladimirov G, Zherebker A, Kononikhin A, Popov I, Nikolaev E. The investigation of the bio-oil produced by hydrothermal liquefaction of Spirulina platensis using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry. Eur J Mass Spectrom (Chichester) 2017; 23:83-88. [PMID: 28657415 DOI: 10.1177/1469066717702648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report the investigation of the hydrothermal liquefaction products of the Spirulina platensis microalgae by using the Fourier transform ion cyclotron resonance mass spectrometry. The hydrothermal liquefaction produced two fractions: one with boiling temperature below 300℃ and the dense residue that remained in the reactor. It was observed that N2 and N classes of compounds that dominate in the positive ESI Fourier transform ion cyclotron resonance spectra for both fractions, and that the light fraction is considerably more saturated then the heavy one. The performed hydrogen/deuterium exchange reaction indicated the presence of the onium compounds in the bio-oil.
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Affiliation(s)
- Yury Kostyukevich
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Mikhail Vlaskin
- 5 Joint Institute for High Temperatures (JIHT) of Russian Academy of Sciences, Moscow, Russia
| | - Gleb Vladimirov
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zherebker
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 6 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Kononikhin
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Igor Popov
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
| | - Eugene Nikolaev
- 1 Skolkovo Institute of Science and Technology, Skolkovo, Russian
- 2 Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Moscow Institute of Physics and Technology, Moscow, Russia
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37
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Zherebker A, Kostyukevich Y, Kononikhin A, Kharybin O, Konstantinov AI, Zaitsev KV, Nikolaev E, Perminova IV. Enumeration of carboxyl groups carried on individual components of humic systems using deuteromethylation and Fourier transform mass spectrometry. Anal Bioanal Chem 2017; 409:2477-2488. [PMID: 28138744 DOI: 10.1007/s00216-017-0197-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/20/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Here, we report a novel approach to enumeration of carboxylic groups carried by individual molecules of humic substances using selective chemical modification and isotopic labeling (deuteromethylation) and high-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS). Esterification was conducted with a use of thionyl chloride-deuteromethanol reagent under mild conditions to avoid transesterification. The deuteromethylated products were subjected to solid phase extraction using PPL Bond Elute cartridges prior to FTICR MS analysis. An amount of carboxyl groups in the individual molecular component was estimated from the length of identified deuteromethylation series. The method allowed for discerning between compounds with close elemental compositions possessing different protolytic properties. We found that different carboxylic moieties occupy distinct regions in molecular space of humic substances (HS) projected onto Van Krevelen diagram. These locations do not depend on the source of the humic material and can be assigned to carboxyl-rich alicyclic molecules (5 to 6 COOH), hydrolyzable tannins (3-4 COOH), lignins (1 to 2 COOH), condensed tannins and lignans (0 to 1 COOH), and carbohydrates (0 COOH). At the same time, the alignment pattern of these carboxylated species along the structural evolution lines in Van Krevelen diagrams was characteristic to the specific transformation processes undergone by the humic materials in the different environments. The obtained data enable mapping of molecular ensemble of HS with regards to their specific acidic compartments and might be used for directed fractionation of HS. Graphical abstract Selective isotopic labeling followed by FTICR MS enables discerning between humic molecules with close elemental compositions carrying different numbers of carboxylic groups.
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Affiliation(s)
- Alexander Zherebker
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991, Moscow, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, 143025, Skolkovo, Moscow Region, Russia.,Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia.,Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38-2, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 9, Institutskii per., 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Alexey Kononikhin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia.,Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38-2, 119334, Moscow, Russia.,Moscow Institute of Physics and Technology, 9, Institutskii per., 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, 143025, Skolkovo, Moscow Region, Russia.,Moscow Institute of Physics and Technology, 9, Institutskii per., 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Andrey I Konstantinov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991, Moscow, Russia
| | - Kirill V Zaitsev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991, Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, 143025, Skolkovo, Moscow Region, Russia. .,Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, 119121, Moscow, Russia. .,Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38-2, 119334, Moscow, Russia. .,Moscow Institute of Physics and Technology, 9, Institutskii per., 141700, Dolgoprudnyi, Moscow Region, Russia.
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991, Moscow, Russia.
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38
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Kostyukevich Y, Solovyov S, Kononikhin A, Popov I, Nikolaev E. The investigation of the bitumen from ancient Greek amphora using FT ICR MS, H/D exchange and novel spectrum reduction approach. J Mass Spectrom 2016; 51:430-436. [PMID: 27270866 DOI: 10.1002/jms.3769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/18/2016] [Accepted: 03/26/2016] [Indexed: 06/06/2023]
Abstract
Recently Russian archeologists have discovered on Taman peninsula an ancient (V B.C.) Greek amphora full of dense bitumen. This is the oldest amphora in the world that contains bitumen. We report the investigation of this bitumen using ultrahigh resolution Fourier transform mass spectrometry. Also we used recently developed in-ESI source Hydrogen/Deuterium exchange approach for the structural characterization of the individual molecules and estimation of the biodegradation of the bitumen. The increase of number of the labile hydrogens compared to the non-degraded oil can serve as an additional evidence of the degradation of bitumen via oxidation. For the facilitation of the spectrum processing we have developed the special iterative spectrum reduction approach. It was observed that molecules that have only oxygen heteroatoms possess two -OH groups what is unusual for the petroleum. Based on this we suggested that the bitumen degraded during its being in amphora for 2500 years. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Sergey Solovyov
- Institute for the History of Material Culture, Dvortsovaya Naberezhnaya, 18, Saint Petersburg, 191186, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr 38 k.2, 119334, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
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Zherebker A, Kostyukevich Y, Kononikhin A, Roznyatovsky VA, Popov I, Grishin YK, Perminova IV, Nikolaev E. High desolvation temperature facilitates the ESI-source H/D exchange at non-labile sites of hydroxybenzoic acids and aromatic amino acids. Analyst 2016; 141:2426-34. [DOI: 10.1039/c5an02676h] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
H/D exchange coupled with high-resolution mass spectrometry has become a powerful analytical approach for structural investigations of complex organic matrices.
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Affiliation(s)
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology
- Skolkovo 143025
- Russian Federation
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences
- 119334 Moscow
| | - Alexey Kononikhin
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences
- 119334 Moscow
- Russia
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences
- 119334 Moscow
| | | | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences
- 119334 Moscow
- Russia
- Moscow Institute of Physics and Technology
- 141700 Dolgoprudnyi, Moscow Region
| | - Yuri K. Grishin
- Lomonosov Moscow State University
- Department of Chemistry
- 119991 Moscow
- Russia
| | - Irina V. Perminova
- Lomonosov Moscow State University
- Department of Chemistry
- 119991 Moscow
- Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology
- Skolkovo 143025
- Russian Federation
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences
- 119334 Moscow
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40
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Chagovets V, Kononikhin A, Starodubtseva N, Kostyukevich Y, Popov I, Frankevich V, Nikolaev E. Peculiarities of data interpretation upon direct tissue analysis by Fourier transform ion cyclotron resonance mass spectrometry. Eur J Mass Spectrom (Chichester) 2016; 22:123-126. [PMID: 27553733 DOI: 10.1255/ejms.1425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The importance of high-resolution mass spectrometry for the correct data interpretation of a direct tissue analysis is demonstrated with an example of its clinical application for an endometriosis study. Multivariate analysis of the data discovers lipid species differentially expressed in different tissues under investigation. High-resolution mass spectrometry allows unambiguous separation of peaks with close masses that correspond to proton and sodium adducts of phosphatidylcholines and to phosphatidylcholines differing in double bond number.
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Affiliation(s)
- Vtaliy Chagovets
- Department of System Biology in Reproduction, Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology", 4 Oparin Street, Moscow 117997, Russian Federation
| | - Aleksey Kononikhin
- Department of System Biology in Reproduction, Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology", 4 Oparin Street, Moscow 117997, Russian Federation. >Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation
| | - Nataliia Starodubtseva
- Department of System Biology in Reproduction, Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology", 4 Oparin Street, Moscow 117997, Russian Federation. >Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation
| | - Yury Kostyukevich
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskii pr., 38, bld. 2 Moscow, 119334, Russian Federation. Skolkovo Institute of Science and Technology, 100 Novaya Street, Skolkovo 143025 Russian Federation
| | - Igor Popov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. nstitute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskii pr., 38, bld. 2 Moscow, 119334, Russian Federation
| | - Vladimir Frankevich
- Department of System Biology in Reproduction, Federal State Budget Institution "Research Center for Obstetrics, Gynecology and Perinatology", 4 Oparin street, Moscow 117997, Russian Federation.
| | - Eugene Nikolaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskii pr., 38, bld. 2 Moscow, 119334, Russian Federation. Skolkovo Institute of Science and Technology, 100 Novaya Street, Skolkovo 143025 Russian Federation
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41
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Kostyukevich Y, Borisova L, Kononikhin A, Popov I, Kukaev E, Nikolaev E. Thermal desorption combined with atmospheric pressure photo ionization for the analysis of volatile compounds and its possible applications. Eur J Mass Spectrom (Chichester) 2016; 22:313-317. [PMID: 27900861 DOI: 10.1255/ejms.1442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report an approach to study volatile organic compounds based on thermal desorption combined with atmospheric pressure photo ionization. The approach allows the sequential evaporation of different fractions of the sample, which simplifies the mass spectrum. We have applied the developed method for the detection of petroleum in vegetable oil. We have shown that in the negative mode, ions of fatty acids corresponding to vegetable oil dominates, while in the positive mode under relatively low temperature the light fraction of petroleum rapidly evaporates making it easy detectable.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation and Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia.
| | - Ludmila Borisova
- National Research University Higher School of Economics, 20 Miasnitskaya Ulitsa, Moscow 101000, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Kukaev
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation and Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia and Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia and Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia
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42
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Kostyukevich Y, Zherebker A, Kononikhin A, Indeykina M, Popov I, Nikolaev E. Letter: Electron-capture dissociation and collision-induced dissociation fragmentation of the supermetallized complexes of Substance P with potassium, cesium and silver. Eur J Mass Spectrom (Chichester) 2016; 22:91-95. [PMID: 27419902 DOI: 10.1255/ejms.1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report the investigation of the collision-induced dissociation (CID) and electron-capture dissociation (ECD) product fragmentations of the supermetallized complexes of Substance P and several monovalent metals. The supermetallization is the phenomenon of the formation of the complex ion peptide-metals in the gas phase when the peptide accepts an unexpectedly large number of metals. We have obtained and investigated complexes with the incorporation of up to four cesium (Cs), up to five potassium (K) and up to six silver (Ag) atoms. The current research reveals crucial changes in the complex behavior in the cases of different metals. It was observed that in CID spectra of complexes with Cs and K is dominated by the peak corresponding to the loss of metal cation while ECD gives a rich fragmentation. In the case of complexes with Ag, the loss of Ag(+) occurs in ECD while the CID shows a good fragmentation.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation..
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory 1-3, 119991 Moscow, Russian Federation..
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Maria Indeykina
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation..
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Kostyukevich Y, Kononikhin A, Kukaev E, Shiea J, Popov I, Nikolaev E. Letter: Supermetallization of peptides and proteins with tetravalent metal Th(IV). Eur J Mass Spectrom (Chichester) 2016; 22:39-42. [PMID: 26863074 DOI: 10.1255/ejms.1405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Supermetallization is the recently observed phenomenon of the formation of complex ions of peptide-metal in the gas phase when the peptide accepts an unexpectedly large number of metal atoms. It has been found that supermetallization takes place during electrospray ionization when charged droplets are evaporating at relatively high temperature (ca 400°C). In the present paper, we demonstrate supermetallized complexes of small protein ubiquitin and two peptides with Th(IV). We have observed complexes of ubiquitin with up to five thorium atoms, and attaching each Th(IV) requires the removal of four hydrogen atoms. To our knowledge, this is the first demonstration of gas-phase complexes of peptides and proteins with tetravalent metal atoms..
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Eugene Kukaev
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
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Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. Conformations of cationized linear oligosaccharides revealed by FTMS combined with in-ESI H/D exchange. J Mass Spectrom 2015; 50:1150-6. [PMID: 26456784 DOI: 10.1002/jms.3633] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/16/2015] [Accepted: 07/11/2015] [Indexed: 05/22/2023]
Abstract
Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in-electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in-ESI source H/D exchange experiments with peptides and proteins.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, Russian Academy of Sciences, Dolgoprudnyi, Moscow Region, 141700, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, Russian Academy of Sciences, Dolgoprudnyi, Moscow Region, 141700, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, Russian Academy of Sciences, Dolgoprudnyi, Moscow Region, 141700, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology, Russian Academy of Sciences, Dolgoprudnyi, Moscow Region, 141700, Russia
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Kostyukevich Y, Kononikhin A, Popov I, Indeykina M, Kozin SA, Makarov AA, Nikolaev E. Supermetallization of peptides and proteins during electrospray ionization. J Mass Spectrom 2015; 50:1079-1087. [PMID: 28338253 DOI: 10.1002/jms.3622] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 04/26/2015] [Accepted: 05/26/2015] [Indexed: 06/06/2023]
Abstract
The formation of metal-peptide complexes during electrospray ionization (ESI) is a widely known phenomenon and is often considered to be undesirable. Such effect considerably limits the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide compounds that are present in the solution and play critical roles in many bioprocesses such as progression of neurodegenerative diseases. In the article, it is demonstrated that under specific conditions such as high temperature of the desolvating capillary, an interesting effect, which can be called as 'supermetallization', occurs. Using a model peptide Αβ amyloid domain 1-16, it was observed that an increase in the temperature of the desolvating capillary results in multiple substitutions of hydrogen atoms by Zn atoms in this peptide. At high temperatures (T ~ 400 °C), up to 11 zinc atoms can be covalently bound to (1-16) Αβ. It was observed that supermetallization of (1-16) Αβ depends on the solvent composition and pH. Supermetallization was also demonstrated for proteins, such as ubiquitin and cytochrome C. That proves that the supermetallization is a general phenomenon for peptides and proteins. For the structural investigation of supermetallized complexes, electron-capture dissociation (ECD) fragmentation was applied. The effect of hydrogen rearranging during ECD was observed. In addition, quantum chemical calculations were used to estimate the possible structures of different supermetallized complexes. These results allow a more deep understanding of the limitations of the use of ESI mass spectrometry for the investigation of biologically relevant metal-peptide complexes. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Maria Indeykina
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow, Russia
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Kostyukevich Y, Zhdanova E, Kononikhin A, Popov I, Kukaev E, Nikolaev E. Observation of the multiple halogenation of peptides in the electrospray ionization source. J Mass Spectrom 2015; 50:899-905. [PMID: 26349644 DOI: 10.1002/jms.3599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/11/2015] [Accepted: 03/27/2015] [Indexed: 06/05/2023]
Abstract
The chlorination of peptides and proteins is an important posttranslational modification, which is a physiological signature of an enzyme myeloperoxidase and can serve as a potential biomarker of some diseases (Parkinson's disease, Alzheimer's disease, etc.). The quantification of the chlorinated peptides has been very challenging in part due to their low levels and artifacts associated with sample preparation. One of the most convenient and promising methods to detect and investigate the chlorinated peptides in the biological samples is the electrospray ionization (ESI) mass spectrometry coupled to the fragmentation techniques (collision-induced dissociation and electron capture dissociation/electron transfer dissociation). We have shown that if the chlorine anions are present in the solution, then the peptide can undergo the chlorination during the ESI ionization. The effect was found to depend on the values of electric potentials of metal parts of the ESI interface. It was found that the grounding of ESI syringe results in the formation of an additional electric loop leading to the electrolytic production of Cl2 and as a consequence the hypochlorous acid inside the ESI needle. Hypochlorous acid reacts with amino groups of peptides and proteins producing chloramine or causing the protein cleavage. In the paper, it is shown on the example of the solution of the several peptides in the presence of HCl that by manipulating the ESI syringe potential, it is possible to create complexes with up to five Cl atoms for sample peptides when the ESI is operated in the positive mode.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Ekaterina Zhdanova
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
| | - Igor Popov
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
| | - Eugene Kukaev
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russia
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334, Moscow, Russia
- Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Kosygina st. 4, 119334, Moscow, Russia
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Vladimirov G, Kostyukevich Y, Hendrickson CL, Blakney GT, Nikolaev E. Effect of magnetic field inhomogeneity on ion cyclotron motion coherence at high magnetic field. Eur J Mass Spectrom (Chichester) 2015; 21:443-449. [PMID: 26307725 DOI: 10.1255/ejms.1375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A three-dimensional code based on the particle-in-cell algorithm modified to account for the inhomogeneity of the magnetic field was applied to determine the effect of Z(1), Z(2), Z(3), Z(4), X, Y, ZX, ZY, XZ(2) YZ(2), XY and X(2)-Y(2) components of an orthogonal magnetic field expansion on ion motion during detection in an FT-ICR cell. Simulations were performed for magnetic field strengths of 4.7, 7, 14.5 and 21 Tesla, including experimentally determined magnetic field spatial distributions for existing 4.7 T and 14.5 T magnets. The effect of magnetic field inhomogeneity on ion cloud stabilization ("ion condensation") at high numbers of ions was investigated by direct simulations of individual ion trajectories. Z(1), Z(2), Z(3) and Z(4) components have the largest effect (especially Z(1)) on ion cloud stability. Higher magnetic field strength and lower m/z demand higher relative magnetic field homogeneity to maintain cloud coherence for a fixed time period. The dependence of mass resolving power upper limit on Z(1) inhomogeneity is evaluated for different magnetic fields and m/z. The results serve to set the homogeneity requirements for various orthogonal magnetic field components (shims) for future FT-ICR magnet design.
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Affiliation(s)
- Gleb Vladimirov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia. Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. Institute for Energy Problems of Chemical Physics, Russian Academy of Science, Moscow, Russia.
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia. Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. Institute for Energy Problems of Chemical Physics, Russian Academy of Science, Moscow, Russia..
| | - Christopher L Hendrickson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA. Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306, USA..
| | - Greg T Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia. Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. Institute for Energy Problems of Chemical Physics, Russian Academy of Science, Moscow, Russia. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Moscow, Russia. V.N. Orekhovich Institute of Biomedical Chemistry, Moscow, Russia Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia..
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Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. Letter: Observation of the 16O/18O exchange during electrospray ionization. Eur J Mass Spectrom (Chichester) 2015; 21:109-113. [PMID: 26181285 DOI: 10.1255/ejms.1373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Isotopic exchange approach coupled to high-resolution mass spectrometry has become the power analytical approach for a wide range of analytical and bioanalyticall applications. Considerable efforts have been dedicated to developing fast exchange techniques directly in the ionization source. But all such methods are limited to the hydrogen/deuterium exchange approaches. In this paper we demonstrate that certain types of oxygen atoms can also be exchanged for (18)O on the time scale of the ionization process. Using HIO(3) and NaIO(4) and by infusing the heavy water H(2)(18)O in the ESI source we have demonstrated that it is possible to obtain a high level of oxygen exchange. It was observed that the rate of this exchange depends to a large extent on the temperature of the desolvating capillary of the mass spectrometer. Several other species, such as peptides, oligonucleotides and low weight organic molecules, were subjected to in-ESI (16)O/(18)O exchange but the exchange was not observed.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Igor Popov
- Emanuel Institute for Biochemical Physics Russian Academy of Sciences Kosygina st. 4, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025 Russian Federation. Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russia. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russia..
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Kostyukevich Y, Kononikhin A, Popov I, Starodubtzevad N, Pekov S, Kukaev E, Indeykina M, Nikolaev E. Letter: Analytical potential of the in-electrospray ionization source hydrogen/deuterium exchange for the investigation of oligonucleotides. Eur J Mass Spectrom (Chichester) 2015; 21:59-63. [PMID: 25906036 DOI: 10.1255/ejms.1330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It has previously been reported that different conformations of oligonucleotides may be detected using a gas-phase hydrogen/deuterium (H/D) exchange performed in the collision cell of a mass spectrometer. The presence of different conformers was postulated based on the bimodal shape of the deuterium distribution and on the ion mobility spectrometry data. Here we implement an in-electrospray ionization source H/D exchange to detect the different conformations of oligonucleotides in the region of ion formation. We observed that the number of H/D exchanges depends considerably on the temperature of the desolvating capillary and varies from 25% at 50°C to 80% at 450°C, but no bimodality in the shape of the deuterium distribution was observed. Such results indicate that in the region of ion formation different conformations of oligonucleotide ions rapidly interconvert one into another.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Novaya St. 100, Skolkovo 143025, Russian Federation. Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Alexey Kononikhin
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
| | - Igor Popov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences, Kosygina St. 4, 119334 Moscow, Russian Federation.
| | - Natalia Starodubtzevad
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. Research Center for Obstetrics, Gynecology and Perinatology, 4 Oparin St., Moscow 117997, Russian Federation.
| | - Stanislav Pekov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation..
| | - Eugene Kukaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation. Emanuel Institute for Biochemical Physics Russian Academy of Sciences, Kosygina St. 4, 119334 Moscow, Russian Federation.
| | - Maria Indeykina
- Institute for Energy Problems of Chemical Physics Russian Academy of Sciences Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation.
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Novaya St. 100, Skolkovo 143025, Russian Federation. Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russian Federation. Moscow Institute of Physics and Technology, 141700 Dolgoprudnyi, Moscow Region, Russian Federation.
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Kostyukevich Y, Kononikhin A, Popov I, Spasskiy A, Nikolaev E. In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange. J Mass Spectrom 2015; 50:49-55. [PMID: 25601674 DOI: 10.1002/jms.3535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/17/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Transition of proteins from the solution to the gas phase during electrospray ionization remains a challenging problem despite the large amount of attention it has received during the past few decades. One of the major questions relates to the extent to which proteins in the gas phase retain their condensed phase structures. We have used in-electrospray source hydrogen/deuterium exchange to determine the number of deuterium incorporations as a function of protein mass, charge state and temperature of the desolvating capillary where the reaction occurs. All experiments were performed on a Thermo LTQ FT Ultra equipped with a 7-T superconducting magnet. Ions were generated by an IonMax Electrospray ion source operated in the positive ESI mode. Deuterium exchange was performed by introducing a droplet of D2 O beneath the ESI capillary. We systematically investigated gas phase hydrogen/deuterium (H/D) exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa. We observed that almost all proteins demonstrate similar exchange rates for all charge states and that these rates increase exponentially with the temperature of the desolvating capillary. We did not observe any clear correlation of the number of H/D exchanges with the value of the cross section for a corresponding charge state. We have demonstrated the possibility of performing in-ESI source H/D exchange of large proteins under atmospheric pressure. The simplicity of the experimental setup makes it a useful experimental technique that can be applied for the investigation of gas phase conformations of proteins.
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Affiliation(s)
- Yury Kostyukevich
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr., 38k.2, 119334, Moscow, Russia; Moscow Institute of Physics and Technology, 141700, Dolgoprudnyi, Moscow Region, Russia; Skolkovo Institute of Science and Technology, Novaya St., 100, Skolkovo, 143025, Russian Federation
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