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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] [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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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] [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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3
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Damont A, Olivier MF, Warnet A, Lyan B, Pujos-Guillot E, Jamin EL, Debrauwer L, Bernillon S, Junot C, Tabet JC, Fenaille F. Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:567-582. [PMID: 31083780 DOI: 10.1002/jms.4372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Nowadays, high-resolution mass spectrometry is widely used for metabolomic studies. Thanks to its high sensitivity, it enables the detection of a large range of metabolites. In metabolomics, the continuous quest for a metabolite identification as complete and accurate as possible has led during the last decade to an ever increasing development of public MS databases (including LC-MS data) concomitantly with bioinformatic tool expansion. To facilitate the annotation process of MS profiles obtained from biological samples, but also to ease data sharing, exchange, and exploitation, the standardization and harmonization of the way to describe and annotate mass spectra seemed crucial to us. Indeed, under electrospray (ESI) conditions, a single metabolite does not produce a unique ion corresponding to its protonated or deprotonated form but could lead to a complex mixture of signals. These MS signals result from the existence of different natural isotopologues of the same compound and also to the potential formation of adduct ions, homomultimeric and heteromultimeric ions, fragment ions resulting from "prompt" in-source dissociations. As a joint reflection process within the French Infrastructure for Metabolomics and Fluxomics (MetaboHUB) and with the purpose of developing a robust and exchangeable annotated MS database made from pure reference compounds (chemical standards) analysis, it appeared to us that giving the metabolomics community some clues to standardize and unambiguously annotate each MS feature was a prerequisite to data entry and further efficient querying of the mass spectral database. The use of a harmonized notation is also mandatory for interlaboratory MS data exchange. Additionally, thorough description of the variety of MS signals arising from the analysis of a unique metabolite might provide greater confidence on its annotation.
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Affiliation(s)
- Annelaure Damont
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Marie-Françoise Olivier
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Anna Warnet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Bernard Lyan
- Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, INRA, UNH, F-63000, Clermont-Ferrand, France
| | - Estelle Pujos-Guillot
- Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, INRA, UNH, F-63000, Clermont-Ferrand, France
| | - Emilien L Jamin
- Toxalim (Research Centre in Food Toxicology), Metatoul-AXIOM platform, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Metatoul-AXIOM platform, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux-MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
- CNRS, Institut Parisien de Chimie Moléculaire, IPCM, Sorbonne Université, 75005, Paris, France
| | - François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191, Gif-sur-Yvette, France
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Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry. Anal Bioanal Chem 2019; 411:3331-3339. [DOI: 10.1007/s00216-019-01802-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/19/2019] [Accepted: 03/22/2019] [Indexed: 10/26/2022]
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Kostyukevich Y, Acter T, Zherebker A, Ahmed A, Kim S, Nikolaev E. Hydrogen/deuterium exchange in mass spectrometry. MASS SPECTROMETRY REVIEWS 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] [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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6
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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] [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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7
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Kostyukevich YI, Kononikhin AS, Indeykina MI, Popov IA, Bocharov KV, Spassky AI, Kozin SA, Makarov AA, Nikolaev EN. Secondary structure of Aβ(1–16) complexes with zinc: A study in the gas phase using deuterium/hydrogen exchange and ultra-high-resolution mass spectrometry. Mol Biol 2017. [DOI: 10.1134/s0026893317030104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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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. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:152-155. [PMID: 29028389 DOI: 10.1177/1469066717718836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [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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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. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:204-209. [PMID: 28152260 DOI: 10.1002/jms.3917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [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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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. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:83-88. [PMID: 28657415 DOI: 10.1177/1469066717702648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [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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Kostyukevich YI, Kononikhin AS, Popov IA, Bugrova AE, Starodubtseva NL, Nikolaev EN. Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916060096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kostyukevich Y, Yacovlev P, Kononikhin A, Popov I, Bugrova A, Starodubtzeva N, Nikolaev E. The use of H/D exchange for secondary structure characterization of supermetallized complexes of ubiquitin with cerium(III). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016040117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Evaporation of the charged droplets in the heating flow tube under atmospheric pressure: observation of the H/D exchange and supermetallization. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.09.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kostyukevich YI, Kharybin ON, Kononikhin AS, Popov IA, Nikolaev EN. Deuterium–hydrogen exchange reactions in peptides and polyatomic organic compounds, as studied on an ion cyclotron resonance mass spectrometer equipped with an ion trap with dynamic harmonization. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kostyukevich YI, Kononikhin AS, Popov IA, Indeykina MI, Nikolaev EN. Supermetallization of Substance P during electrospray ionization. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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] [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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17
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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. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 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] [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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18
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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. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:91-95. [PMID: 27419902 DOI: 10.1255/ejms.1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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19
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Kukaev EN, Kononikhin AS, Starodubtseva NL, Kostyukevich YI, Popova IA, Chagovets V, Nagornov KO, Nikolaev EN. Atmospheric pressure thermal ionization ion source for peptide analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:307-311. [PMID: 27900860 DOI: 10.1255/ejms.1443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel atmospheric pressure thermal ionization (APTI) ion source was developed for the analysis of liquid samples. The feasibility of the ion source was demonstrated on peptides using two configurations-assisted by hot wire or hot surface. Microalloyed molybdenum, used as a thermal ion- emitter, notably facilitated the formation of multiply-charged ions, but fragmentation products were still observed. Peptide fragmentation accompanying thermal ionization can be used for peptide identification. The described method is promising for studies of biological samples with minimal pre-treatment.
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Affiliation(s)
- Eugenii N Kukaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Natalia L Starodubtseva
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Yury I Kostyukevich
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and Skolkovo Institute of Science and Technology, 143025 Skolkovo, Moscow region, Russian Federation
| | - Igor A Popova
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vitaliy Chagovets
- V.I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Konstantin O Nagornov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Eugene N Nikolaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russian Federation and Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation and Skolkovo Institute of Science and Technology, 143025 Skolkovo, Moscow region, Russian Federation
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20
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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. JOURNAL OF MASS SPECTROMETRY : JMS 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] [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, Kononikhin A, Popov I, Nikolaev E. Letter: Observation of the 16O/18O exchange during electrospray ionization. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 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] [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. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 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] [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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23
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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. JOURNAL OF MASS SPECTROMETRY : JMS 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] [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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Enumeration of non-labile oxygen atoms in dissolved organic matter by use of 16O/18O exchange and Fourier transform ion-cyclotron resonance mass spectrometry. Anal Bioanal Chem 2014; 406:6655-64. [DOI: 10.1007/s00216-014-8097-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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