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Zherebker AY, Rukhovich GD, Kharybin ON, Fedoros EI, Perminova IV, Nikolaev EN. Fourier transform ion cyclotron resonance mass spectrometry for the analysis of molecular composition and batch-to-batch consistency of plant-derived polyphenolic ligands developed for biomedical application. Rapid Commun Mass Spectrom 2020; 34:e8850. [PMID: 32492216 DOI: 10.1002/rcm.8850] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
UNLABELLED Complex plant-derived polyphenols are promising for biomedical application. Their high complexity prevents the use of conventional pharmacopoeia techniques to perform quality control. The goal of this study was to apply ultra-high-resolution mass spectrometry to evaluate the batch-to-batch consistency of the molecular composition of a polyphenolic ligand using appropriate statistical metrics. METHODS Polyphenols were obtained by hydrolyzed-lignin oxidation. Manufacturing was performed under a range of reaction conditions: heating cycles, oxygen flows, purification. Direct-injection Fourier transform ion cyclotron resonance mass spectrometry (DI FTICR-MS) was applied to analyze reaction products. For pairwise comparison Jaccard and Tanimoto similarities calculations were proposed. In addition, principal component analysis (PCA) was applied for sample grouping based on the molecular class contributions. RESULTS FTICR-MS analysis revealed moderate Jaccard similarity of products synthesized under the same conditions, which shared about 50% of the formulae calculated in each sample. The intensity-based Tanimoto index indicated high similarity of major components distribution of samples synthesized under standard conditions, while products obtained with variations in synthetic conditions were significantly different. PCA of molecular class contributions showed similar grouping with a high cumulative score. CONCLUSIONS FTICR-MS provides robust metrics for the examination of batch-to-batch consistency of synthetic polyphenol materials. This approach can be proposed for the analysis of reference samples and for development of complementary methods for quality control of medicinal agents based on various biologically active matrices.
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Affiliation(s)
- Alexander Ya Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Gleb D Rukhovich
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg N Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg, 197758, Russia
- Nobel LTD, Saint-Petersburg, 192012, Russia
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
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Abstract
Phosphorylation is one of the most common posttranslational modification (PTM) of proteins. Main challenge of phosphoprotein detection is their low abundance comparing to abundance of unmodified proteins. The method of selected reactions monitoring (SRM) allows to perform very sensitive and selective analysis of desired PTMs. Using myelin basic protein (MBP) as a model we have developed a method for phosphoprotein detection by SRM. The method is based on obtaining of phosphoproteins in a reconstituted kinase system and following usage these phosphorylated protein as a template for the development of the SRM method. The developed method was successfully applied for detection of phosphopeptides of myelin basic protein in the samples of human brain glioma.
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Affiliation(s)
| | - V G Zgoda
- Orekhovich Institute of Biomedical Chemistry (IBMC)
| | - O N Kharybin
- Orekhovich Institute of Biomedical Chemistry (IBMC)
| | - E N Nikolaev
- Orekhovich Institute of Biomedical Chemistry (IBMC); Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
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Kolesanova EF, Sanzhakov MA, Kharybin ON. Development of the schedule for multiple parallel "difficult" Peptide synthesis on pins. Int J Pept 2013; 2013:197317. [PMID: 24027588 PMCID: PMC3762146 DOI: 10.1155/2013/197317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022]
Abstract
Unified schedule for multiple parallel solid-phase synthesis of so-called "difficult" peptides on polypropylene pins was developed. Increase in the efficiency of 9-fluorenyl(methoxycarbonyl) N-terminal amino-protecting group removal was shown to have a greater influence on the accuracy of the "difficult" peptide synthesis than the use of more efficient amino acid coupling reagents such as aminium salts. Hence the unified schedule for multiple parallel solid-phase synthesis of "difficult" peptides included the procedure for N-terminal amino group deprotection modified by applying a more efficient reagent for the deprotection and the standard procedure of amino acid coupling by carbodiimide method with an additional coupling using aminium salts, if necessary. Amino acid coupling with the help of carbodiimide allows to follow the completeness of the coupling via the bromophenol blue indication, thus providing the accuracy of the synthesis and preventing an overexpenditure of expensive reagents. About 100 biotinylated hepatitis C virus envelope protein fragments, most of which represented "difficult" peptides, were successfully obtained by synthesis on pins with the help of the developed unified schedule.
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Affiliation(s)
- Ekaterina F. Kolesanova
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
| | - Maxim A. Sanzhakov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
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Galetskiy DN, Lohscheider JN, Kononikhin AS, Kharybin ON, Popov IA, Adamska I, Nikolaev EN. Light stress photodynamics of chlorophyll-binding proteins in Arabidopsis thaliana thylakoid membranes revealed by high-resolution mass spectrometric studies. Bioorg Khim 2011; 37:119-31. [PMID: 21460887 DOI: 10.1134/s1068162011010079] [Citation(s) in RCA: 4] [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: 11/23/2022]
Abstract
In higher plants the light energy is captured by the photosynthetic pigments that are bound to photosystem I and II and their light-harvesting complex (LHC) subunits. In this study, we examined the photodynamic changes within chlorophyll-protein complexes in the thylakoid membrane of Arabidopsis thaliana leaves adapted to low light and subsequently exposed to light stress. Chlorophyll-protein complexes were isolated using sucrose density gradient centrifugation and blue-native polyacrylamid gel electrophoresis (BN-PAGE). Proteome analysis was performed using SDS-PAGE, HPLC and high resolution mass spectrometry. We identified several rarely expressed and stress-induced chlorophyll-binding proteins, showed changes in localization of early light-induced protein family and LHC protein family members between different photosynthetic complexes and assembled/disassembled subcomplexes under light stress conditions and discuss their role in a variety of light stress-related processes.
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Affiliation(s)
- D N Galetskiy
- Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
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Indeykina MI, Popov IA, Kozin SA, Kononikhin AS, Kharybin ON, Tsvetkov PO, Makarov AA, Nikolaev EN. Capabilities of MS for Analytical Quantitative Determination of the Ratio of α- and βAsp7 Isoforms of the Amyloid-β Peptide in Binary Mixtures. Anal Chem 2011; 83:3205-10. [DOI: 10.1021/ac103213j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria I. Indeykina
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Alexey S. Kononikhin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Philippe O. Tsvetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Evgenij N. Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
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Aleshina EI, Pyndyk NV, Moĭsa AA, Sanzhakov MA, Kharybin ON, Nikolaev EN, Kolesanova EF. [Synthesis of beta-amyloid fragment 5RHDSGY10 and its isomers]. Biomed Khim 2008; 54:184-191. [PMID: 18522220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Peptide RHDSGY that represents the fragment of human beta-amyloid Zn-binding site and its isomers RH(D-Asp)SGY and RH(beta-Asp)SGY have been prepared by solid-phase synthesis and analysed by HPLC and various mass-spectrometric methods. The problem of low yield of peptide RHDSGY and its isomers attributed to 9-fluorenylmethoxycarbonyl (Fmoc)-amino acids and/or formation of side-products as RH(Asp-imide)SGY and RHDSGY (instead of RH(beta-Asp)SGY) was solved via selection of reagents for the removal of Fmoc groups from the growing peptide chain.
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Vilkov AN, Gamage CM, Misharin AS, Doroshenko VM, Tolmachev DA, Tarasova IA, Kharybin ON, Novoselov KP, Gorshkov MV. Atmospheric pressure ionization permanent magnet fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 2007; 18:1552-8. [PMID: 17587594 PMCID: PMC2041863 DOI: 10.1016/j.jasms.2007.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 05/15/2007] [Accepted: 05/15/2007] [Indexed: 05/16/2023]
Abstract
A new Fourier transform ion cyclotron resonance mass spectrometer based on a permanent magnet with an atmospheric pressure ionization source was designed and constructed. A mass resolving power (full-width-at-half-maximum) of up to 80,000 in the electron ionization mode and 25,000 in the electrospray mode was obtained. Also, a mass measurement accuracy at low-ppm level has been demonstrated for peptide mixtures in a mass range of up to 1200 m/z in the isotopically resolved mass spectra.
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Popov IA, Chen H, Kharybin ON, Nikolaev EN, Cooks RG. Detection of explosives on solid surfaces by thermal desorption and ambient ion/molecule reactions. Chem Commun (Camb) 2005:1953-5. [PMID: 15834469 DOI: 10.1039/b419291e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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
A simple, fast and direct method is presented for detecting traces of solid explosives on cotton swabs or in particulate samples: ions are transferred into a mass spectrometer after thermal desorption and corona discharge chemical ionization in ambient air; specificity is enhanced using ambient ion/molecule reactions or by conventional tandem mass spectrometry.
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Affiliation(s)
- Igor A Popov
- Department of Chemistry, 560 Oval Drive, Purdue University, West Lafayette, IN 47907, USA
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Torbeev VY, Lyssenko KA, Kharybin ON, Antipin MY, Kostyanovsky RG. Lamellar Racemic Twinning as an Obstacle for the Resolution of Enantiomers by Crystallization: The Case of Me(All)N+(CH2Ph)Ph X- (X = Br, I) Salts. J Phys Chem B 2003. [DOI: 10.1021/jp035588l] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vladimir Yu. Torbeev
- N. N. Semenov Institute of Chemical Physics, A. N. Nesmeyanov Institute of Organoelement Compounds, and Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin A. Lyssenko
- N. N. Semenov Institute of Chemical Physics, A. N. Nesmeyanov Institute of Organoelement Compounds, and Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Oleg N. Kharybin
- N. N. Semenov Institute of Chemical Physics, A. N. Nesmeyanov Institute of Organoelement Compounds, and Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Mikhail Yu. Antipin
- N. N. Semenov Institute of Chemical Physics, A. N. Nesmeyanov Institute of Organoelement Compounds, and Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Remir G. Kostyanovsky
- N. N. Semenov Institute of Chemical Physics, A. N. Nesmeyanov Institute of Organoelement Compounds, and Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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Kostyanovsky RG, Nikolaev EN, Kharybin ON, Kadorkina GK, Kostyanovsky VR. Pasteur-like resolution of quasi-racemates in solid and gas phases. Mendeleev Communications 2003. [DOI: 10.1070/mc2003v013n03abeh001801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kravchenko AN, Kadorkina GK, Sigachev AS, Maksareva EY, Lyssenko KA, Belyakov PA, Lebedev OV, Kharybin ON, Makhova NN, Kostyanovsky RG. Spontaneous resolution in the imidazolidin-2-one series. Mendeleev Communications 2003. [DOI: 10.1070/mc2003v013n03abeh001736] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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