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Sorokin AA, Pekov SI, Zavorotnyuk DS, Shamraeva MM, Bormotov DS, Popov IA. Modern machine-learning applications in ambient ionization mass spectrometry. Mass Spectrom Rev 2024. [PMID: 38671553 DOI: 10.1002/mas.21886] [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: 12/12/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
This article provides a comprehensive overview of the applications of methods of machine learning (ML) and artificial intelligence (AI) in ambient ionization mass spectrometry (AIMS). AIMS has emerged as a powerful analytical tool in recent years, allowing for rapid and sensitive analysis of various samples without the need for extensive sample preparation. The integration of ML/AI algorithms with AIMS has further expanded its capabilities, enabling enhanced data analysis. This review discusses ML/AI algorithms applicable to the AIMS data and highlights the key advancements and potential benefits of utilizing ML/AI in the field of mass spectrometry, with a focus on the AIMS community.
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Affiliation(s)
- Anatoly A Sorokin
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav I Pekov
- Mass Spectrometry Laboratory, Skolkovo Institute of Science and Technology, Moscow, Russia
- Translational Medicine Laboratory, Siberian State Medical University, Tomsk, Russia
- Department for Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis S Zavorotnyuk
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mariya M Shamraeva
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis S Bormotov
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor A Popov
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Translational Medicine Laboratory, Siberian State Medical University, Tomsk, Russia
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2
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Pekov SI, Bormotov DS, Bocharova SI, Sorokin AA, Derkach MM, Popov IA. Mass spectrometry for neurosurgery: Intraoperative support in decision-making. Mass Spectrom Rev 2024. [PMID: 38571445 DOI: 10.1002/mas.21883] [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: 12/12/2023] [Revised: 02/29/2024] [Accepted: 03/23/2024] [Indexed: 04/05/2024]
Abstract
Ambient ionization mass spectrometry was proved to be a powerful tool for oncological surgery. Still, it remains a translational technique on the way from laboratory to clinic. Brain surgery is the most sensitive to resection accuracy field since the balance between completeness of resection and minimization of nerve fiber damage determines patient outcome and quality of life. In this review, we summarize efforts made to develop various intraoperative support techniques for oncological neurosurgery and discuss difficulties arising on the way to clinical implementation of mass spectrometry-guided brain surgery.
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Affiliation(s)
- Stanislav I Pekov
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
- Siberian State Medical University, Tomsk, Russian Federation
| | - Denis S Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | | | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Maria M Derkach
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
- Siberian State Medical University, Tomsk, Russian Federation
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3
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Dolbnya AD, Popov IA, Pekov SI. Molecular Biomarkers in Cholangiocarcinoma: Focus on Bile. Curr Top Med Chem 2024; 24:CTMC-EPUB-138255. [PMID: 38303538 DOI: 10.2174/0115680266290367240130054142] [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: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Hepatobiliary system cancers have demonstrated an increasing incidence rate in the past years. Without the presence of early symptoms, the majority of such cancers manifest with a set of similar symptoms, such as cholestasis resulting in posthepatic icterus. Differential diagnosis of hepatobiliary cancers is required for the therapy selection, however, the similarity of the symptoms complicates diagnostics. Thus, the search for molecular markers is of high interest for such patients. Cholangiocarcinoma (CCA) is characterized by a poor prognosis due to a low resectability rate, which occurs because this disease is frequently beyond the limits of surgical therapy at the time of diagnosis. The CCA is diagnosed by the combination of clinical/biochemical features, radiological methods, and non-specific serum tumor biomarkers, although invasive examination is still needed. The main disadvantage is limited specificity and sensitivity, which complicates early diagnostics. Therefore, prognostic and predictive biomarkers are still lacking and urgently needed for early diagnosis. In contrast to serum, bile is more accessible to identify biliary disease due to its simpler composition. Moreover, bile can contain higher concentrations of tumor biomarkers due to its direct contact with the tumor. It is known that the composition of the main bile component - bile acids, may vary during different diseases of the biliary tract. This review summarizes the recent developments in the current research on the diagnostic biomarkers for CCA in serum and bile and provides an overview of the methods of bile acids analysis.
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Affiliation(s)
- Andrey D Dolbnya
- Siberian State Medical University, Tomsk 634050, Russian Federation
| | - Igor A Popov
- Siberian State Medical University, Tomsk 634050, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russian Federation
| | - Stanislav I Pekov
- Siberian State Medical University, Tomsk 634050, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russian Federation
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
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Kechko OI, Adzhubei AA, Tolstova AP, Indeykina MI, Popov IA, Zhokhov SS, Gnuchev NV, Mitkevich VA, Makarov AA, Kozin SA. Molecular Mechanism of Zinc-Dependent Oligomerization of Alzheimer's Amyloid-β with Taiwan (D7H) Mutation. Int J Mol Sci 2023; 24:11241. [PMID: 37511001 PMCID: PMC10378775 DOI: 10.3390/ijms241411241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Amyloid-β (Aβ) is a peptide formed by 39-43 amino acids, heterogenous by the length of its C-terminus. Aβ constitutes a subnanomolar monomeric component of human biological fluids; however, in sporadic variants of Alzheimer's disease (AD), it forms soluble neurotoxic oligomers and accumulates as insoluble extracellular polymeric aggregates (amyloid plaques) in the brain tissues. The plaque formation is controlled by zinc ions; therefore, abnormal interactions between the ions and Aβ seem to take part in the triggering of sporadic AD. The amyloid plaques contain various Aβ isoforms, among which the most common is Aβ with an isoaspartate in position 7 (isoD7). The spontaneous conversion of D7 to isoD7 is associated with Aβ aging. Aβ molecules with isoD7 (isoD7-Aβ) easily undergo zinc-dependent oligomerization, and upon administration to transgenic animals (mice, nematodes) used for AD modeling, act as zinc-dependent seeds of the pathological aggregation of Aβ. The formation of zinc-bound homo- and hetero-oligomers with the participation of isoD7-Aβ is based on the rigidly structured segment 11-EVHH-14, located in the Aβ metal binding domain (Aβ16). Some hereditary variants of AD are associated with familial mutations within the domain. Among these, the most susceptible to zinc-dependent oligomerization is Aβ with Taiwan (D7H) mutation (D7H-Aβ). In this study, the D7H-Aβ metal binding domain (D7H-Aβ16) has been used as a model to establish the molecular mechanism of zinc-induced D7H-Aβ oligomerization through turbidimetry, dynamic light scattering, isothermal titration calorimetry, mass spectrometry, and computer modelling. Additionally, the modeling data showed that a molecule of D7H-Aβ, as well as isoD7-Aβ in combination with two Aβ molecules, renders a stable zinc-induced heterotrimer. The trimers are held together by intermolecular interfaces via zinc ions, with the primary interfaces formed by 11-EVHH-14 sites of the interacting trimer subunits. In summary, the obtained results confirm the role of the 11-EVHH-14 region as a structure and function determinant for the zinc-dependent oligomerization of all known Aβ species (including various chemically modified isoforms and AD-associated mutants) and point at this region as a potent target for drugs aimed to stop amyloid plaque formation in both sporadic and hereditary variants of AD.
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Affiliation(s)
- Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria I Indeykina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Sergey S Zhokhov
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Nikolay V Gnuchev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Bormotov DS, Eliferov VA, Peregudova OV, Zavorotnyuk DS, Bocharov KV, Pekov SI, Sorokin AA, Nikolaev EN, Popov IA. Incorporation of a Disposable ESI Emitter into Inline Cartridge Extraction Mass Spectrometry Improves Throughput and Spectra Stability. J Am Soc Mass Spectrom 2023; 34:119-122. [PMID: 36535019 DOI: 10.1021/jasms.2c00207] [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: 06/17/2023]
Abstract
Rapid and reliable methods for detecting tumor margins are crucial for neuro-oncology. Several mass spectrometry-based methods have been recently proposed to address this problem. Inline Cartridge Extraction (ICE) demonstrates the potential for clinical application, based on ex-vivo analysis of dissected tissues, but requires time-consuming steps to avoid cross-contamination. In this work, a method of incorporating a disposable electrospray emitter into the ICE cartridge by PEEK sleeves melting is developed. It reduces total analysis time and improves throughput. The proposed setup also improves the robustness of the ICE molecular profiling as demonstrated with human glial tumor samples in that stability and reproducibility of the spectra were increased.
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Affiliation(s)
- Denis S Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Vasily A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Olga V Peregudova
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Denis S Zavorotnyuk
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Konstantin V Bocharov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - Stanislav I Pekov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russian Federation
- Siberian State Medical University, Tomsk 634050, Russian Federation
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russian Federation
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
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Kuzin AA, Stupnikova GS, Strelnikova PA, Danichkina KV, Indeykina MI, Pekov SI, Popov IA. Quantitative Assessment of Serine-8 Phosphorylated β-Amyloid Using MALDI-TOF Mass Spectrometry. Molecules 2022; 27:molecules27238406. [PMID: 36500498 PMCID: PMC9740911 DOI: 10.3390/molecules27238406] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The study of the molecular mechanisms of the pathogenesis of Alzheimer's disease (AD) is extremely important for identifying potential therapeutic targets as well as early markers. In this regard, the study of the role of post-translational modifications (PTMs) of β-amyloid (Aβ) peptides is of particular relevance. Serine-8 phosphorylated forms (pSer8-Aβ) have been shown to have an increased aggregation capacity and may reflect the severity of amyloidosis. Here, an approach for quantitative assessment of pSer8-Aβ based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed. The relative fraction of pSer8-Aβ was estimated in the total Aβ-pool with a detection limit of 1 fmol for pSer8-Aβ (1-16) and an accuracy of 2% for measurements in the reflectron mode. The sensitivity of the developed method is suitable for determining the proportion of phosphorylated peptides in biological samples.
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Affiliation(s)
- Andrey A. Kuzin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | | | - Polina A. Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | | | - Maria I. Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
| | - Stanislav I. Pekov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia
- Siberian State Medical University, 634050 Tomsk, Russia
- Correspondence: (S.I.P.); (I.A.P.)
| | - Igor A. Popov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Siberian State Medical University, 634050 Tomsk, Russia
- Correspondence: (S.I.P.); (I.A.P.)
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Bormotov DS, Shamraeva MA, Kuzin AA, Shamarina EV, Eliferov VA, Silkin SV, Zhdanova EV, Pekov SI, Popov IA. Ambient ms profiling of meningiomas: intraoperative oncometabolite-based monitoring. BRSMU 2022. [DOI: 10.24075/brsmu.2022.072] [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: 01/13/2023]
Abstract
The primary method of initial treatment of meningiomas is radical neurosurgical intervention. Various methods of intraoperative diagnostics currently in development aim to improve resection efficiency; we focus on methods based on molecular profiling using ambient ionization mass spectrometry. Such methods have been proven effective on various tumors, but the specifics of the molecular structure and the mechanical properties of meningiomas raise the question of applicability of protocols developed for other conditions for this particular task. The study aimed to compare the potential clinical use of three methods of ambient ionization in meningioma sample analysis: spray from tissue, inline cartridge extraction, and touch spherical sampler probe spray. To this end, lipid and metabolic profiles of meningioma tissues removed in the course of planned neurosurgical intervention have been analyzed. It is shown that in clinical practice, the lipid components of the molecular profile are best analyzed using the inline cartridge extraction method, distinguished by its ease of implementation and highest informational value. Analysis of oncometabolites with low molecular mass is optimally performed with the touch spherical sampler probe spray method, which scores high in both sensitivity and mass-spectrometric complex productivity.
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Affiliation(s)
- DS Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - MA Shamraeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - AA Kuzin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - EV Shamarina
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - VA Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - SV Silkin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - EV Zhdanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - SI Pekov
- Skoltech, Moscow, Russia; Siberian State Medical University, Tomsk, Russia
| | - IA Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Pekov SI, Zhvansky ES, Eliferov VA, Sorokin AA, Ivanov DG, Nikolaev EN, Popov IA. Determination of Brain Tissue Samples Storage Conditions for Reproducible Intraoperative Lipid Profiling. Molecules 2022; 27:molecules27082587. [PMID: 35458785 PMCID: PMC9029908 DOI: 10.3390/molecules27082587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Ex-vivo molecular profiling has recently emerged as a promising method for intraoperative tissue identification, especially in neurosurgery. The short-term storage of resected samples at room temperature is proposed to have negligible influence on the lipid molecular profiles. However, a detailed investigation of short-term molecular profile stability is required to implement molecular profiling in a clinic. This study evaluates the effect of storage media, temperature, and washing solution to determine conditions that provide stable and reproducible molecular profiles, with the help of ambient ionization mass spectrometry using rat cerebral cortex as model brain tissue samples. Utilizing normal saline for sample storage and washing media shows a positive effect on the reproducibility of the spectra; however, the refrigeration shows a negligible effect on the spectral similarity. Thus, it was demonstrated that up to hour-long storage in normal saline, even at room temperature, ensures the acquisition of representative molecular profiles using ambient ionization mass spectrometry.
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Affiliation(s)
- Stanislav I. Pekov
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
- Siberian State Medical University, 634050 Tomsk, Russia
- Correspondence: (S.I.P.); (E.N.N); (I.A.P.)
| | - Evgeny S. Zhvansky
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
| | - Vasily A. Eliferov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
| | - Anatoly A. Sorokin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
- Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Daniil G. Ivanov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
| | - Eugene N. Nikolaev
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Correspondence: (S.I.P.); (E.N.N); (I.A.P.)
| | - Igor A. Popov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.S.Z.); (V.A.E.); (A.A.S.); (D.G.I.)
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov, 117997 Moscow, Russia
- Correspondence: (S.I.P.); (E.N.N); (I.A.P.)
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Zakharova NV, Kononikhin AS, Indeykina MI, Bugrova AE, Strelnikova P, Pekov S, Kozin SA, Popov IA, Mitkevich V, Makarov AA, Nikolaev EN. Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer's disease. Mass Spectrom Rev 2022:e21775. [PMID: 35347731 DOI: 10.1002/mas.21775] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
This review covers the results of the application of mass spectrometric (MS) techniques to study the diversity of beta-amyloid (Aβ) peptides in human samples. Since Aβ is an important hallmark of Alzheimer's disease (AD), which is a socially significant neurodegenerative disorder of the elderly worldwide, analysis of its endogenous variations is of particular importance for elucidating the pathogenesis of AD, predicting increased risks of the disease onset, and developing effective therapy. MS approaches have no alternative for the study of complex samples, including a wide variety of Aβ proteoforms, differing in length and modifications. Approaches based on matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography with electrospray ionization tandem MS are most common in Aβ studies. However, Aβ forms with isomerized and/or racemized Asp and Ser residues require the use of special methods for separation and extra sensitive and selective methods for detection. Overall, this review summarizes current knowledge of Aβ species found in human brain, cerebrospinal fluid, and blood plasma; focuses on application of different MS approaches for Aβ studies; and considers the potential of MS techniques for further studies of Aβ-peptides.
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Affiliation(s)
- Natalia V Zakharova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kononikhin
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Polina Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav Pekov
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- N.N. Semenov Federal Center of Chemical Physics, V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Zhvansky ES, Eliferov VA, Sorokin AA, Shurkhay VA, Pekov SI, Bormotov DS, Ivanov DG, Zavorotnyuk DS, Bocharov KV, Khaliullin IG, Belenikin MS, Potapov AA, Nikolaev EN, Popov IA. Assessment of variation of inline cartridge extraction mass spectra. J Mass Spectrom 2021; 56:e4640. [PMID: 32798239 DOI: 10.1002/jms.4640] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/15/2020] [Revised: 07/20/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Recently, mass-spectrometry methods show its utility in tumor boundary location. The effect of differences between research and clinical protocols such as low- and high-resolution measurements and sample storage have to be understood and taken into account to transfer methods from bench to bedside. In this study, we demonstrate a simple way to compare mass spectra obtained by different experimental protocols, assess its quality, and check for the presence of outliers and batch effect in the dataset. We compare the mass spectra of both fresh and frozen-thawed astrocytic brain tumor samples obtained with the inline cartridge extraction prior to electrospray ionization. Our results reveal the importance of both positive and negative ion mode mass spectrometry for getting reliable information about sample diversity. We show that positive mode highlights the difference between protocols of mass spectra measurement, such as fresh and frozen-thawed samples, whereas negative mode better characterizes the histological difference between samples. We also show how the use of similarity spectrum matrix helps to identify the proper choice of the measurement parameters, so data collection would be kept reliable, and analysis would be correct and meaningful.
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Affiliation(s)
- Evgeny S Zhvansky
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Vasiliy A Eliferov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Anatoly A Sorokin
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Vsevolod A Shurkhay
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
- Outpatient department, Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Stanislav I Pekov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Denis S Bormotov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Daniil G Ivanov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Denis S Zavorotnyuk
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Konstantin V Bocharov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Iliyas G Khaliullin
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Maksim S Belenikin
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Aleksandr A Potapov
- Outpatient department, Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Evgeny N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Igor A Popov
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
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11
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Pekov SI, Bormotov DS, Nikitin PV, Sorokin AA, Shurkhay VA, Eliferov VA, Zavorotnyuk DS, Potapov AA, Nikolaev EN, Popov IA. Rapid estimation of tumor cell percentage in brain tissue biopsy samples using inline cartridge extraction mass spectrometry. Anal Bioanal Chem 2021; 413:2913-2922. [PMID: 33751161 DOI: 10.1007/s00216-021-03220-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 10/21/2022]
Abstract
Tumor cell percentage (TCP) is an essential characteristic of biopsy samples that directly affects the sensitivity of molecular testing in clinical practice. Apart from clarifying diagnoses, rapid evaluation of TCP combined with various neuronavigation systems can be used to support decision making in neurosurgery. It is known that ambient mass spectrometry makes it possible to rapidly distinguish healthy from malignant tissues. In connection with this, here we demonstrate the possibility of using non-imaging ambient mass spectrometry to evaluate TCP in glial tumor tissues with a high degree of confidence. Molecular profiles of histologically annotated human glioblastoma tissue samples were obtained using the inline cartridge extraction ambient mass spectrometry approach. XGBoost regressors were trained to evaluate tumor cell percentage. Using cross-validation, it was estimated that the TCP was determined by the regressors with a precision of approximately 90% using only low-resolution data. This result demonstrates that ambient mass spectrometry provides an accurate method todetermine TCP in dissected tissues even without implementing mass spectrometry imaging. The application of such techniques offers the possibility to automate routine tissue screening and TCP evaluation to boost the throughput of pathology laboratories. Rapid estimation of tumor cell percentage during neurosurgery.
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Affiliation(s)
- Stanislav I Pekov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143026, Russian Federation.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Denis S Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Pavel V Nikitin
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Vsevolod A Shurkhay
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation.,N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Vasiliy A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Denis S Zavorotnyuk
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Alexander A Potapov
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143026, Russian Federation
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation.
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12
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Pekov SI, Sorokin AA, Kuzin AA, Bocharov KV, Bormotov DS, Shivalin AS, Shurkhay VA, Potapov AA, Nikolaev EN, Popov IA. [Analysis of phosphatidylcholines alterations in human glioblastoma multiform tissues ex vivo]. Biomed Khim 2021; 67:81-87. [PMID: 33645525 DOI: 10.18097/pbmc20216701081] [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: 11/23/2022]
Abstract
Significant metabolism alteration is accompanying the cell malignization process. Energy metabolism disturbance leads to the activation of de novo synthesis and beta-oxidation processes of lipids and fatty acids in a cancer cell, which becomes an indicator of pathological processes inside the cell. The majority of studies dealing with lipid metabolism alterations in glial tumors are performed using the cell lines in vitro or animal models. However, such conditions do not entirely represent the physiological conditions of cell growth or possible cells natural variability. This work presents the results of the data obtained by applying ambient mass spectrometry to human glioblastoma multiform tissues. By analyzing a relatively large cohort of primary and secondary glioblastoma samples, we identify the alterations in cells lipid composition, which accompanied the development of grade IV brain tumors. We demonstrate that primary glioblastomas, as well as ones developed from astrocytomas, are enriched with mono- and diunsaturated phosphatidylcholines (PC 26:1, 30:2, 32:1, 32:2, 34:1, 34:2). Simultaneously, the saturated and polyunsaturated phosphatidylcholines and phosphatidylethanolamines decrease. These alterations are obviously linked to the availability of the polyunsaturated fatty acids and activation of the de novo lipid synthesis and beta-oxidation pathways under the anaerobic conditions in the tumor core.
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Affiliation(s)
- S I Pekov
- Skolkovo Institute of Science and Technology, Moscow, Russia; Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
| | - A A Sorokin
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
| | - A A Kuzin
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
| | - K V Bocharov
- Semenov Federal Center of Chemical Physic of RAS, Moscow, Russia
| | - D S Bormotov
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
| | - A S Shivalin
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
| | - V A Shurkhay
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia; N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - A A Potapov
- N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - I A Popov
- Moscow Institute of Physics and Technology (National Research University), Moscow, Russia
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13
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Zhvansky ES, Ivanov DG, Sorokin AA, Bugrova AE, Nikolaev EN, Popov IA. Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging. Anal Chem 2021; 93:3706-3709. [PMID: 33591173 DOI: 10.1021/acs.analchem.1c00437] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we demonstrate a new approach for interactively assessing hyperspectral data spatial structures for heterogeneity using mass spectrometry imaging. This approach is based on the visualization of the cosine distance as the similarity levels between mass spectra of a chosen region and the rest of the image (sample). The applicability of the method is demonstrated on a set of mass spectrometry images of frontal mouse brain slices. Selection of the reference pixel of the mass spectrometric image and a further view of the corresponding cosine distance map helps to prepare supporting vectors for further analysis, select features, and carry out biological interpretation of different tissues in the mass spectrometry context with or without histological annotation. Visual inspection of the similarity maps reveals the spatial distribution of features in tissue samples, which can serve as the molecular histological annotation of a slide.
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Affiliation(s)
- Evgeny S Zhvansky
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Daniil G Ivanov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Institute of Cell Biophysics RAS, Institutskaya st., 3, 142290 Pushchino, Russia.,Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Anna E Bugrova
- Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street, 100, 143025 Skolkovo, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
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14
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Zhvansky ES, Sorokin AA, Bormotov DS, Bocharov KV, Zavorotnyuk DS, Ivanov DG, Nikolaev EN, Popov IA. The software for interactive evaluation of mass spectra stability and reproducibility. Bioinformatics 2020; 37:140-142. [PMID: 33367588 DOI: 10.1093/bioinformatics/btaa1072] [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] [Received: 08/20/2020] [Revised: 11/25/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Mass spectrometry methods are widely used for the analysis of biological and medical samples. Recently developed methods such as DESI, REIMS, NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here we present SSM Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra. AVAILABILITY Source code, example datasets, binaries, and other information are available at https://github.com/EvgenyZhvansky/R_matrix. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- E S Zhvansky
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
| | - A A Sorokin
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
| | - D S Bormotov
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
| | - K V Bocharov
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
| | - D S Zavorotnyuk
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
| | - D G Ivanov
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia.,Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - I A Popov
- Dolgoprudny, Moscow Institute of Physics and Technology, Russia
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15
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Eliferov VA, Zhvansky ES, Sorokin AA, Shurkhay VA, Bormotov DS, Pekov SI, Nikitin PV, Ryzhova MV, Kulikov EE, Potapov AA, Nikolaev EN, Popov IA. [The role of lipids in the classification of astrocytoma and glioblastoma using MS tumor profiling]. Biomed Khim 2020; 66:317-325. [PMID: 32893821 DOI: 10.18097/pbmc20206604317] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for determining the molecular composition of the analyzed objects it eliminates the influence of mutual ion suppression. Despite significant progress in the field of direct MS of biological tissues, the question of mass spectrometric profile attribution to a certain type of tissue still remains open. The use of modern machine learning methods and protocols (e.g., "random forests") enables us to trace possible relationships between the components of the sample MS profile and the result of brain tumor tissue classification (astrocytoma or glioblastoma). It has been shown that the most pronounced differences in the mass spectrometric profiles of these tumors are due to their lipid composition. Detection of statistically significant differences in lipid profiles of astrocytoma and glioblastoma may be used to perform an express test during surgery and inform the neurosurgeon what type of malignant tissue he is working with. The ability to accurately determine the boundaries of the neoplastic growth significantly improves the quality of both surgical intervention and postoperative rehabilitation, as well as the duration and quality of life of patients.
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Affiliation(s)
- V A Eliferov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - E S Zhvansky
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - A A Sorokin
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - V A Shurkhay
- N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - D S Bormotov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - S I Pekov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - P V Nikitin
- N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - M V Ryzhova
- N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - E E Kulikov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia; Federal Research Center "Fundamentals of Biotechnology", RAS, Moscow, Russia
| | - A A Potapov
- N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - I A Popov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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16
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Ivanov DG, Indeykina MI, Pekov SI, Bugrova AE, Kechko OI, Iusupov AE, Kononikhin AS, Makarov AA, Nikolaev EN, Popov IA. Relative Quantitation of Beta-Amyloid Peptide Isomers with Simultaneous Isomerization of Multiple Aspartic Acid Residues by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:164-168. [PMID: 32881518 DOI: 10.1021/jasms.9b00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry can be used for rapid quantitation of peptides with various post-translational modifications (PTM), even if they do not shift the mass of the native peptide. Previously, it was shown that MALDI-TOF MS can be used for quantitation of isoD7 beta-amyloid 1-42 peptide. On the basis of the differences in the collision-induced dissociation fragmentation pattern of native Aβ, isoD7 Aβ, isoD23 Aβ, and isoD7_23 peptide (a di-isomerized peptide with both isomerization of D7 and D23 residues), we developed a MALDI-TOF-based method for simultaneous quantitation of all of these isoforms. Using multivariate regression for analysis of fragment MS data, the method allows the determination of the molar fractions of all of these isoforms with up to 16% error for mixtures with 2 pmol total amount of the beta-amyloid peptide.
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Affiliation(s)
- Daniil G Ivanov
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Stanislav I Pekov
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Akademika Oparina ul. 4, 117198 Moscow, Russia
| | - Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova ul. 32, 119991 Moscow, Russia
| | - Adel E Iusupov
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- Skolkovo Institute of Science and Technology, Novaya Street 100, 143025 Skolkovo, Moscow Region, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova ul. 32, 119991 Moscow, Russia
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street 100, 143025 Skolkovo, Moscow Region, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Akademika Oparina ul. 4, 117198 Moscow, Russia
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17
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Pekov SI, Eliferov VA, Sorokin AA, Shurkhay VA, Zhvansky ES, Vorobyev AS, Potapov AA, Nikolaev EN, Popov IA. Inline cartridge extraction for rapid brain tumor tissue identification by molecular profiling. Sci Rep 2019; 9:18960. [PMID: 31831871 PMCID: PMC6908710 DOI: 10.1038/s41598-019-55597-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/03/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022] Open
Abstract
The development of perspective diagnostic techniques in medicine requires efficient high-throughput biological sample analysis methods. Here, we present an inline cartridge extraction that facilitates the screening rate of mass spectrometry shotgun lipidomic analysis of tissue samples. We illustrate the method by its application to tumor tissue identification in neurosurgery. In perspective, this high-performance method provides new possibilities for the investigation of cancer pathogenesis and metabolic disorders.
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Affiliation(s)
- Stanislav I Pekov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Vasily A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Vsevolod A Shurkhay
- Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Evgeny S Zhvansky
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Alexander S Vorobyev
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Alexander A Potapov
- Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation.
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18
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Kononikhin AS, Brzhozovskiy AG, Ryabokon AM, Fedorchenko K, Zakharova NV, Spasskii AI, Popov IA, Ilyin VK, Solovyova ZO, Pastushkova LK, Polyakov AV, Varfolomeev SD, Larina IM, Nikolaev EN. Proteome Profiling of the Exhaled Breath Condensate after Long-Term Spaceflights. Int J Mol Sci 2019; 20:E4518. [PMID: 31547269 PMCID: PMC6770753 DOI: 10.3390/ijms20184518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/21/2019] [Revised: 08/22/2019] [Accepted: 09/10/2019] [Indexed: 11/21/2022] Open
Abstract
Comprehensive studies of the effects of prolonged exposure to space conditions and the overload experienced during landing on physiological and biochemical changes in the human body are extremely important in the context of planning long-distance space flights, which can be associated with constant overloads and various risk factors for significant physiological changes. Exhaled breath condensate (EBC) can be considered as a valuable subject for monitoring physiological changes and is more suitable for long-term storage than traditional monitoring subjects such as blood and urine. Herein, the EBC proteome changes due to the effects of spaceflight factors are analyzed. Thirteen EBC samples were collected from five Russian cosmonauts (i) one month before flight (background), (ii) immediately upon landing modules in the field (R0) after 169-199 days spaceflights, and (iii) on the seventh day after landing (R+7). Semi-quantitative label-free EBC proteomic analysis resulted in 164 proteins, the highest number of which was detected in EBC after landing (R0). Pathways enrichment analysis using the GO database reveals a large group of proteins which take part in keratinization processes (CASP14, DSG1, DSP, JUP, and so on). Nine proteins (including KRT2, KRT9, KRT1, KRT10, KRT14, DCD, KRT6C, KRT6A, and KRT5) were detected in all three groups. A two-sample Welch's t-test identified a significant change in KRT2 and KRT9 levels after landing. Enrichment analysis using the KEGG database revealed the significant participation of detected proteins in pathogenic E. coli infection (ACTG1, TUBA1C, TUBA4A, TUBB, TUBB8, and YWHAZ), which may indicate microbiota changes associated with being in space. This assumption is confirmed by microbial composition analysis. In general, the results suggest that EBC can be used for noninvasive monitoring of health status and respiratory tract pathologies during spaceflights, and that the obtained data are important for the development of medicine for use in extreme situations. Data are available from ProteomeXchange using the identifier PXD014191.
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Affiliation(s)
- Alexey S Kononikhin
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia.
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Alexander G Brzhozovskiy
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna M Ryabokon
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kristina Fedorchenko
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia.
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Natalia V Zakharova
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander I Spasskii
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vyacheslav K Ilyin
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Zoya O Solovyova
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Lyudmila Kh Pastushkova
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey V Polyakov
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey D Varfolomeev
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Larina
- Russian Federation State Scientific Research Center Institute of Biomedical Problems, Russian Academy of Sciences, 119991 Moscow, Russia.
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia.
| | - Evgeny N Nikolaev
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia.
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19
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Pekov SI, Ivanov DG, Bugrova AE, Indeykina MI, Zakharova NV, Popov IA, Kononikhin AS, Kozin SA, Makarov AA, Nikolaev EN. Evaluation of MALDI-TOF/TOF Mass Spectrometry Approach for Quantitative Determination of Aspartate Residue Isomerization in the Amyloid-β Peptide. J Am Soc Mass Spectrom 2019; 30:1325-1329. [PMID: 31073890 DOI: 10.1007/s13361-019-02199-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 09/24/2018] [Revised: 03/11/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
Immunoprecipitation (IP) combined with MALDI-TOF mass spectrometry is a powerful instrument for peptide and protein identification in biological samples. In this study, the analytical capabilities of MALDI-TOF/TOF mass spectrometry for relative quantitation of isoAsp7 in Aβ(1-42) and Aβ(1-16) were investigated. The possibility of quantitative determination of isoAsp7 in Aβ(1-42) with the detection limit as low as 2 pmol has been demonstrated. The same approach was applied for a shorter peptide Aβ(1-16) and resulted in enhanced accuracy (± 3.2%), and lower detection limit (50 fmol). Pilot experiments with artificial cerebrospinal fluid and mouse brain tissue were performed and showed that the proposed IP-MALDI-TOF/TOF approach could be applied for measuring isoAβ content in biological fluids and tissues. Additionally, it was shown that 6E10 anti-amyloid antibodies might affect the accuracy of the amyloid-β quantitation in the presence of the isomerized peptide.
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Affiliation(s)
- Stanislav I Pekov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
| | - Daniil G Ivanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Maria I Indeykina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Natalia V Zakharova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.
- V.L. Talrose Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia.
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
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20
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Zhvansky ES, Pekov SI, Sorokin AA, Shurkhay VA, Eliferov VA, Potapov AA, Nikolaev EN, Popov IA. Metrics for evaluating the stability and reproducibility of mass spectra. Sci Rep 2019; 9:914. [PMID: 30696886 PMCID: PMC6351633 DOI: 10.1038/s41598-018-37560-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 07/13/2018] [Accepted: 12/06/2018] [Indexed: 11/15/2022] Open
Abstract
In this work, we demonstrate a new approach for assessing the stability and reproducibility of mass spectra obtained via ambient ionization methods. This method is suitable for both comparing experiments during which only one mass spectrum is measured and for evaluating the internal homogeneity of mass spectra collected over a period of time. The approach uses Pearson’s r coefficient and the cosine measure to compare the spectra. It is based on the visualization of dissimilarities between measurements, thus leading to the analysis of dissimilarity patterns. The cosine measure and correlations are compared to obtain better metrics for spectra homogeneity. The method filters out unreliable scans to prevent the analyzed sample from being wrongly characterized. The applicability of the method is demonstrated on a set of brain tumor samples. The developed method could be employed in neurosurgical applications, where mass spectrometry is used to monitor the intraoperative tumor border.
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Affiliation(s)
- E S Zhvansky
- Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Moscow, Russian Federation
| | - S I Pekov
- Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Moscow, Russian Federation
| | - A A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Moscow, Russian Federation
| | - V A Shurkhay
- Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - V A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Moscow, Russian Federation
| | - A A Potapov
- Federal State Autonomous Institution «N.N. Burdenko National Scientific and Practical Center for Neurosurgery» of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation.
| | - I A Popov
- Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Moscow, Russian Federation
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21
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Zakharova NV, Bugrova AE, Kononikhin AS, Indeykina MI, Popov IA, Nikolaev EN. Mass spectrometry analysis of the diversity of Aβ peptides: difficulties and future perspectives for AD biomarker discovery. Expert Rev Proteomics 2018; 15:773-775. [DOI: 10.1080/14789450.2018.1525296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Natalia V. Zakharova
- Moscow Institute of Physics and Technology, Laboratory of ion and molecular physics, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Anna E. Bugrova
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S. Kononikhin
- Moscow Institute of Physics and Technology, Laboratory of ion and molecular physics, Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Maria I. Indeykina
- Moscow Institute of Physics and Technology, Laboratory of ion and molecular physics, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Igor A. Popov
- Moscow Institute of Physics and Technology, Laboratory of ion and molecular physics, Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Eugene N. Nikolaev
- Moscow Institute of Physics and Technology, Laboratory of ion and molecular physics, Moscow, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, Russia
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22
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Nikitin PV, Potapov AA, Ryzhova MV, Shurkhay VA, Kulikov EE, Zhvanskiy ES, Popov IA, Nikolaev EN. [The role of lipid metabolism disorders, atypical isoforms of protein kinase C, and mutational status of cytosolic and mitochondrial forms of isocitrate dehydrogenase in carcinogenesis of glial tumors]. Zh Vopr Neirokhir Im N N Burdenko 2018; 82:112-120. [PMID: 29927433 DOI: 10.17116/neiro2018823112] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The relationship between molecular genetic and metabolic disorders is one of the challenges of modern oncology. In this review, we consider lipid metabolism and its changes as one of the factors of oncogenesis of glial tumors. Also, we demonstrate that the genome and the metabolome are interconnected by a large number of links, and the metabolic pathways, during their reorganization, are able to drastically affect the genetic structure of the cell and, in particular, cause its tumor transformation. Our own observations and analysis of the literature data allow us to conclude that mass spectrometry is a highly accurate current method for assessing metabolic disorders at the cellular level. The use of mass spectrometry during surgery allows the neurosurgeon to obtain real-time data on the level of specific molecular markers in the resected tissue, thereby bringing intraoperative navigation techniques to the molecular level. The generation of molecular fingerprints for each tumor significantly complements the available neuroimaging, molecular genetic, and immunohistochemical data.
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Affiliation(s)
- P V Nikitin
- Burdenko Neurosurgery Institute, 4-ya Tverskaya-Yamskaya Str., 16, Moscow, Russia, 125047
| | - A A Potapov
- Burdenko Neurosurgery Institute, 4-ya Tverskaya-Yamskaya Str., 16, Moscow, Russia, 125047
| | - M V Ryzhova
- Burdenko Neurosurgery Institute, 4-ya Tverskaya-Yamskaya Str., 16, Moscow, Russia, 125047
| | - V A Shurkhay
- Burdenko Neurosurgery Institute, 4-ya Tverskaya-Yamskaya Str., 16, Moscow, Russia, 125047; Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, Moscow Region, Russia, 141701
| | - E E Kulikov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, Moscow Region, Russia, 141701; Federal Research Center 'Fundamentals of Biotechnology', Leninskiy Prospect, 33/2, Moscow, Russia, 119071
| | - E S Zhvanskiy
- Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, Moscow Region, Russia, 141701
| | - I A Popov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, Moscow Region, Russia, 141701
| | - E N Nikolaev
- Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, Moscow Region, Russia, 141701; Skolkovo Institute of Science and Technology, Nobelya Str., 3, Moscow, Russia, 143026; Institute of Energy Problems of Chemical Physics, Leninskiy Prospect, 38/2, Moscow, Russia, 119334
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23
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Kugaevskaya EV, Veselovsky AV, Indeykina MI, Solovyeva NI, Zharkova MS, Popov IA, Nikolaev EN, Mantsyzov AB, Makarov AA, Kozin SA. N-domain of angiotensin-converting enzyme hydrolyzes human and rat amyloid-β(1-16) peptides as arginine specific endopeptidase potentially enhancing risk of Alzheimer's disease. Sci Rep 2018; 8:298. [PMID: 29321566 PMCID: PMC5762728 DOI: 10.1038/s41598-017-18567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 08/21/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder. Amyloid-β (Aβ) aggregation is likely to be the major cause of AD. In contrast to humans and other mammals, that share the same Aβ sequence, rats and mice are invulnerable to AD-like neurodegenerative pathologies, and Aβ of these rodents (ratAβ) has three amino acid substitutions in the metal-binding domain 1-16 (MBD). Angiotensin-converting enzyme (ACE) cleaves Aβ-derived peptide substrates, however, there are contradictions concerning the localization of the cleavage sites within Aβ and the roles of each of the two ACE catalytically active domains in the hydrolysis. In the current study by using mass spectrometry and molecular modelling we have tested a set of peptides corresponding to MBDs of Aβ and ratAβ to get insights on the interactions between ACE and these Aβ species. It has been shown that the N-domain of ACE (N-ACE) acts as an arginine specific endopeptidase on the Aβ and ratAβ MBDs with C-amidated termini, thus assuming that full-length Aβ and ratAβ can be hydrolyzed by N-ACE in the same endopeptidase mode. Taken together with the recent data on the molecular mechanism of zinc-dependent oligomerization of Aβ, our results suggest a modulating role of N-ACE in AD pathogenesis.
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Affiliation(s)
| | | | - Maria I Indeykina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.,Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | | | | | - Igor A Popov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.,Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia
| | - Eugene N Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow Region, Russia.,Skolkovo Institute of Science and technology, Moscow, Russia
| | - Alexey B Mantsyzov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia.
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24
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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 (Mosk) 2017; 51:710-716. [PMID: 28900091 DOI: 10.7868/s0026898417030107] [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: 07/03/2016] [Accepted: 09/29/2016] [Indexed: 11/23/2022]
Abstract
Complexes of peptide fragment 1-16 of beta-amyloid with transition metals play an important role in the development of a broad class of neurodegenerative diseases, which determines the interest in investigating the structures of these complexes. In this work, we have applied the method of the deuterium/hydrogen exchange in combination with ultra-high-resolution mass spectrometry to study conformational changes in (1-16) beta-amyloid peptide induced by binding of zinc(II) atoms. The efficiency of the deuterium/hydrogen exchange depended on the number of zinc atoms bound to the peptide and on the temperature of the ionization source region. Deuterium/hydrogen exchange reactions have been performed directly in the ionization source. The number of exchanges decreased considerably with an increasing numbers of zinc atoms. The relationship has been described with a damped exponential curve, which indicated that the binding of zinc atoms altered the conformation of the peptide ion by making it less open, which limits the access to inner areas of the molecule.
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Affiliation(s)
- Yu I Kostyukevich
- Moscow Institute of Physics and Technology (State University), Dolgprudny, Moscow oblast, 141701 Russia.,Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, 143026 Russia
| | - A S Kononikhin
- Moscow Institute of Physics and Technology (State University), Dolgprudny, Moscow oblast, 141701 Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia.,Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia.,
| | - M I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - I A Popov
- Moscow Institute of Physics and Technology (State University), Dolgprudny, Moscow oblast, 141701 Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - K V Bocharov
- Moscow Institute of Physics and Technology (State University), Dolgprudny, Moscow oblast, 141701 Russia.,Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A I Spassky
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia.,Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - S A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E N Nikolaev
- Moscow Institute of Physics and Technology (State University), Dolgprudny, Moscow oblast, 141701 Russia.,Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, 143026 Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia.,Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
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25
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Sysoev AA, Popov IA. Editorial. Eur J Mass Spectrom (Chichester) 2017; 23:129. [PMID: 29028393 DOI: 10.1177/1469066717722296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Alexey A Sysoev
- 1 National Research Nuclear University MEPhI, Moscow, Russia
| | - Igor A Popov
- 2 Moscow Institute of Physics and Technology (State University), Moscow, Russia
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26
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Brzhozovskiy A, Kononikhin A, Indeykina M, Pastushkova LK, Popov IA, Nikolaev EN, Larina IM. Label-free study of cosmonaut's urinary proteome changes after long-duration spaceflights. Eur J Mass Spectrom (Chichester) 2017; 23:225-229. [PMID: 29028400 DOI: 10.1177/1469066717717610] [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
During the entire time that cosmonauts stay on board the international space station, different extreme space flight factors affect their bodies. In order to find out what physiological changes occur under the influence of spaceflight, different parameters of the human body before and after flights are monitored. Analysis of the urine proteome is one of the most perspective non-invasive methods of condition monitoring. The aim of the study was to perform a comparative semi-quantitative label-free urine proteome analysis of samples collected from 21 cosmonauts before and after long-duration spaceflight at the international space station. For proteomic analysis, urine samples were collected from cosmonauts at three time periods: six months prior to the flight as a background, and on days 1 and 7 of the recovery period after landing. All probes were analyzed by LC-MS/MS, and 256 proteins were identified with more than one unique peptide. The core proteome consists of 50 proteins that are detected in more than 70% of the samples. Label-free semi-quantitative analysis enables us to find 20 proteins which were significantly changed on +1 day and +7 day with respect to background. Most of these proteins participate in the regulation of biological processes, in the regulation of the immune system and in intracellular processes also; some of these proteins are related with stress and response to stimulus. In conclusion, the proteomic analysis of cosmonauts' urine samples provides new data on the human body's adaptation to ground conditions after long-duration spaceflight.
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Affiliation(s)
- A Brzhozovskiy
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
| | - A Kononikhin
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow, Russia
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - M Indeykina
- 3 V.L. Talrose 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
| | - LKh Pastushkova
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
| | - I A Popov
- 2 Moscow Institute of Physics and Technology, Moscow, Russia
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - E N Nikolaev
- 3 V.L. Talrose 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 Skolkovo Institute of Science and Technology, Space Cluster, Skolkovo, Russia
| | - I M Larina
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
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27
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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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28
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Zakharova NV, Shornikova AY, Bugrova AE, Baybakova VV, Indeykina MI, Kononikhin AS, Popov IA, Kechko OI, Makarov AA, Nikolaev EN. Evaluation of plasma peptides extraction methods by high-resolution mass spectrometry. Eur J Mass Spectrom (Chichester) 2017; 23:209-212. [PMID: 29028405 DOI: 10.1177/1469066717720907] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Monitoring of peptides offers a promising approach for the discovery of novel biomarkers, which might be valuable for detection, treatment and prevention of large variety of diseases. Development of highly effective methods for plasma peptide extraction remains an important task. In the current study, we applied different types of plasma peptide extraction approaches to reveal efficient methods which would provide the highest peptide yield. We used different combinations of plasma treatment with acetonitrile and/or urea/guanidine, protein precipitation by acetone, gel-filtration, ultrafiltration, and two types of solid phase extraction. The extracted peptides were analyzed by LC-MS/MS. The obtained results suggest that several methods, including differential solubilization, organic precipitation, as well as some variants of ultrafiltration and solid phase extraction, provide effective plasma peptide enrichment convenient for further LC-MS/MS analysis. Alas, most of the identified peptides were extracted by only one of the applied methods. Hence, it seems reasonable to consider several methods to increase the possibility of novel biomarker discovery.
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Affiliation(s)
- N V Zakharova
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Y Shornikova
- 3 School of chemistry, Department of analytical chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A E Bugrova
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - V V Baybakova
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - M I Indeykina
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - A S Kononikhin
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - I A Popov
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - O I Kechko
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A A Makarov
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E N Nikolaev
- 1 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- 4 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 6 Skolkovo Institute of Science and Technology, Moscow, Russia
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29
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Zhvansky ES, Sorokin AA, Popov IA, Shurkhay VA, Potapov AA, Nikolaev EN. High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors. Eur J Mass Spectrom (Chichester) 2017; 23:213-216. [PMID: 29028390 DOI: 10.1177/1469066717721484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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
The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. Tumor fragments were investigated by the immunohistochemistry method and were identified as necrotic tissue with necrotized vessels, necrotic tissue with tumor stain, tumor with necrosis (tumor tissue as major), tumor, necrotized tumor (necrotic tissues as major), parts of tumor cells, boundary brain tissue, and brain tissue hyperplasia. The technique of classification of tumor tissues based on mass spectrometric profile data processing is suggested in this paper. Classifiers dividing the researched sample to the corresponding tissue type were created as a result of the processing. Classifiers of necrotic and tumor tissues are shown to yield a combined result when the tissue is heterogeneous and consists of both tumor cells and necrotic tissue.
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Affiliation(s)
- E S Zhvansky
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russian Federation
| | - A A Sorokin
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
| | - I A Popov
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
| | - V A 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, Russian Federation
| | - A A 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, Russian Federation
| | - E N Nikolaev
- 1 Moscow Institute of Physics and Technology, Dolgoprudnyy, Moscow Region, Russian Federation
- 2 Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Moscow, Russian Federation
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russian Federation
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30
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Kononikhin AS, Chagovets VV, Starodubtseva NL, Ryndin AY, Bugrova AE, Kostyukevich YI, Popov IA, Frankevich VE, Ionov OV, Sukhikh GT, Nikolaev EN. [Determination of proteomic and metabolic composition of exhaled breath condensate of newborns]. Mol Biol (Mosk) 2017; 50:540-4. [PMID: 27414793 DOI: 10.7868/s0026898416020099] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 11/20/2015] [Indexed: 11/23/2022]
Abstract
Here, the possibility of proteomic and metabolomic analysis of the composition of exhaled breath condensate of neonates with respiratory support. The developed method allows non-invasive collecting sufficient amount of the material for identification of disease-specific biomarkers. Samples were collected by using a condensing device that was incorporated into the ventilation system. The collected condensate was analyzed by liquid chromatography coupled with high resolution mass spectrometry and tandem mass spectrometry. The isolated substances were identified with a use of databases for proteins and metabolites. As a result, a number of compounds that compose the exhaled breath condensate was determined and can be considered as possible biomarkers of newborn diseases or stage of development.
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Affiliation(s)
- A S Kononikhin
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia.,
| | - V V Chagovets
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
| | - N L Starodubtseva
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia
| | - A Y Ryndin
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
| | - A E Bugrova
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia.,Emanuel Institute for Biochemical Physics, Moscow, 119934, Russia
| | - Y I Kostyukevich
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia.,Emanuel Institute for Biochemical Physics, Moscow, 119934, Russia
| | - I A Popov
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia.,Emanuel Institute for Biochemical Physics, Moscow, 119934, Russia
| | - V E Frankevich
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
| | - O V Ionov
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
| | - G T Sukhikh
- Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
| | - E N Nikolaev
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia.,Emanuel Institute for Biochemical Physics, Moscow, 119934, Russia
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Kononikhin AS, Starodubtseva NL, Chagovets VV, Ryndin AY, Burov AA, Popov IA, Bugrova AE, Dautov RA, Tokareva AO, Podurovskaya YL, Ionov OV, Frankevich VE, Nikolaev EN, Sukhikh GT. Exhaled breath condensate analysis from intubated newborns by nano-HPLC coupled to high resolution MS. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1047:97-105. [PMID: 28040456 DOI: 10.1016/j.jchromb.2016.12.036] [Citation(s) in RCA: 22] [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: 03/30/2016] [Revised: 11/01/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022]
Abstract
Invasiveness of examination and therapy methods is a serious problem for intensive care and nursing of premature infants. Exhaled breath condensate (EBC) is the most attractive biofluid for non-invasive methods development in neonatology for monitoring the status of intubated infants. The aim of the study was to propose an approach for EBC sampling and analysis from mechanically ventilated neonates. EBC collection system with good reproducibility of sampling was demonstrated. Discovery-based proteomic and metabolomic studies were performed using nano-HPLC coupled to high resolution MS. Label-free semi-quantitative data were compared for intubated neonates with congenital pneumonia (12 infants) and left-sided congenital diaphragmatic hernia (12 infants) in order to define disease-specific features. Totally 119 proteins and 164 metabolites were found. A number of proteins and metabolites that can act as potential biomarkers of respiratory diseases were proposed and require further validation.
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Affiliation(s)
- A S Kononikhin
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia.
| | - N L Starodubtseva
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - V V Chagovets
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - A Y Ryndin
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - A A Burov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - I A Popov
- Moscow Institute of Physics and Technology, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - A E Bugrova
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - R A Dautov
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - A O Tokareva
- Moscow Institute of Physics and Technology, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Y L Podurovskaya
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - O V Ionov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - V E Frankevich
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - E N Nikolaev
- Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia.
| | - G T Sukhikh
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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32
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Kononikhin AS, Starodubtseva NL, Pastushkova LK, Kashirina DN, Fedorchenko KY, Brhozovsky AG, Popov IA, Larina IM, Nikolaev EN. Spaceflight induced changes in the human proteome. Expert Rev Proteomics 2016; 14:15-29. [PMID: 27817217 DOI: 10.1080/14789450.2017.1258307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts. Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors' research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments. Expert commentary: Overall, the authors believe that the present background, methodology and equipment improvements will enhance spaceflight safety and support accumulation of new knowledge on how organisms adapt to extreme conditions.
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Affiliation(s)
- Alexey S Kononikhin
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia.,b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Natalia L Starodubtseva
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Lyudmila Kh Pastushkova
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Daria N Kashirina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | | | - Alexander G Brhozovsky
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Igor A Popov
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Irina M Larina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Evgeny N Nikolaev
- d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia.,e Emanuel Institute for Biochemical Physics , Russian Academy of Sciences , Moscow , Russia.,f Skolkovo Institute of Science and Technology, Space Cluster , Skolkovo , Russia
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33
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Starodubtseva NL, Kononikhin AS, Bugrova AE, Chagovets V, Indeykina M, Krokhina KN, Nikitina IV, Kostyukevich YI, Popov IA, Larina IM, Timofeeva LA, Frankevich VE, Ionov OV, Degtyarev DN, Nikolaev EN, Sukhikh GT. Investigation of urine proteome of preterm newborns with respiratory pathologies. J Proteomics 2016; 149:31-37. [PMID: 27321582 DOI: 10.1016/j.jprot.2016.06.012] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/23/2016] [Accepted: 06/10/2016] [Indexed: 12/27/2022]
Abstract
A serious problem during intensive care and nursing of premature infants is the invasiveness of many examination methods. Urine is an excellent source of potential biomarkers due to the safety of the collection procedure. The purpose of this study was to determine the features specific for the urine proteome of preterm newborns and their changes under respiratory pathologies of infectious and non-infectious origin. The urine proteome of 37 preterm neonates with respiratory diseases and 10 full-term newborns as a control group were investigated using the LC-MS/MS method. The total number of identified proteins and unique peptides was 813 and 3672 respectively. In order to further specify the defined infant-specific dataset these proteins were compared with urine proteome of healthy adults (11 men and 11 pregnant women) resulting in 94 proteins found only in infants. Pairwise analysis performed for label-free proteomic data revealed 36 proteins which reliably distinguished newborns with respiratory disorders of infectious genesis from those with non-infectious pathologies, including: proteins involved in cell adhesion (CDH-2,-5,-11, NCAM1, TRY1, DSG2), metabolism (LAMP1, AGRN, TPP1, GPX3, APOD, CUBN, IDH1), regulation of enzymatic activity (SERPINA4, VASN, GAPDH), inflammatory and stress response (CD55, CD 93, NGAL, HP, TNFR, LCN2, AGT, S100P, SERPINA1/C1/B1/F1).
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Affiliation(s)
- Natalia L Starodubtseva
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alexey S Kononikhin
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; V.L. Talrose 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, Moscow, Russia
| | - Anna E Bugrova
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vitaliy Chagovets
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Maria Indeykina
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Ksenia N Krokhina
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Irina V Nikitina
- 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, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Igor A Popov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Irina M Larina
- Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - Leila A Timofeeva
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vladimir E Frankevich
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Oleg V Ionov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Dmitry N Degtyarev
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Eugene N Nikolaev
- Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia.
| | - Gennady T Sukhikh
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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Starodubtseva NL, Kononikhin AS, Bugrova AE, Krokhina KN, Nikitina IV, Kostyukevich YI, Popov IA, Frankevich VE, Aleksandrova NV, Ionov OV, Nikolaev EN, Degtyarev DN. Proteomic Analysis of the Urine for Diagnostics in Newborns. Bull Exp Biol Med 2016; 160:867-70. [PMID: 27165075 DOI: 10.1007/s10517-016-3329-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 11/30/2022]
Abstract
Proteomic analysis of the urine was used for noninvasive diagnostics of abnormalities in newborns treated in the neonatal intensive care unit. This approach can be used to differentiate between infectious and noninfectious respiratory disorders.
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Affiliation(s)
- N L Starodubtseva
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia.
| | - A S Kononikhin
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A E Bugrova
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - K N Krokhina
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - I V Nikitina
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Yu I Kostyukevich
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - I A Popov
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - V E Frankevich
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - N V Aleksandrova
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - O V Ionov
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E N Nikolaev
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - D N Degtyarev
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation, Moscow, Russia
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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] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zherebker AY, Airapetyan D, Konstantinov AI, Kostyukevich YI, Kononikhin AS, Popov IA, Zaitsev KV, Nikolaev EN, Perminova IV. Synthesis of model humic substances: a mechanistic study using controllable H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry. Analyst 2016; 140:4708-19. [PMID: 25988201 DOI: 10.1039/c5an00602c] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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
The products of the oxidative coupling of phenols are frequently used as synthetic analogues to natural humic substances (HS) for biomedical research. However, their molecular compositions and exact structures remain largely unknown. The objective of this study was to develop a novel approach for the molecular-level analysis of phenolic polymerisates that is capable of inventorying molecular constituents and resolving their distinct structural formulas. For this purpose, we have synthesized the model HS using the oxidative coupling of a specifically designed phenylpropanoic monomer, 3-(4-hydroxy-3-methoxyphenyl)-3-oxopropionic acid, to hydroquinone. We have characterized the synthesized model HS using high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), (1)H NMR spectroscopy, and controllable hydrogen/deuterium (H/D) exchange. We succeeded in the molecular inventory of the model HS. The assigned molecular formulas occupied the substantial space of CHO compositions in the Van Krevelen diagram with a maximum density found in the regions of tannins and lignins, resembling those of natural HS. To identify the exact structural formulas of the individual constituents in the model HS, we have applied selective H/D exchange of non-labile backbone protons by a choice of basic or acidic catalytic conditions followed by FTICR MS. The determined formulas allowed us to verify the proposed pathways of hydroxylation and carboxylation in the course of the phenolic coupling and to identify the acetylation of aromatic rings as an important side reaction. We conclude that the proposed analytical approach may be used to identify the molecular carriers of biological activity within the phenolic polymerisates and eventually within natural HS.
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Affiliation(s)
- Alexander Ya Zherebker
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1-3, 119991 Moscow, Russia.
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Kononikhin AS, Fedorchenko KY, Ryabokon AM, Starodubtseva NL, Popov IA, Zavialova MG, Anaev EC, Chuchalin AG, Varfolomeev SD, Nikolaev EN. [Proteomic analysis of exhaled breath condensate for diagnosis of pathologies of the respiratory system]. Biomed Khim 2015; 61:777-80. [PMID: 26716752 DOI: 10.18097/pbmc20156106777] [Citation(s) in RCA: 6] [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: 11/23/2022]
Abstract
Study of the proteomic composition of exhaled breath condensate (EBC), is a promising non-invasive method for the diagnosis of the respiratory tract diseases in patients. In this study the EBC proteomic composition of the 79 donors, including patients with different pathologies of the respiratory system has been investigated. Cytoskeletal keratins type II (1, 2, 3, 4, 5, 6) and cytoskeletal keratins the type I (9, 10, 14, 15, 16) were invariant for all samples. Analyzing the frequency of occurrence of proteins in different groups of examined patients, several categories of protein have been recognized: found in all pathologies (Dermcidin, Alpha-1-microglobulin, SHROOM3), found in several pathologies (CSTA, LCN1, JUP, PIP, TXN), and specific for a single pathology (PRDX1, Annexin A1/A2). The EBC analysis by HPLC-MS/MS can be used to identify potential protein markers characteristic for pathologies such as chronic obstructive pulmonary disease (PRDX1) and pneumonia (Annexin A1/A2).
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Affiliation(s)
- A S Kononikhin
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - K Yu Fedorchenko
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A M Ryabokon
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - N L Starodubtseva
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - I A Popov
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - M G Zavialova
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - E C Anaev
- Research Institute of Pulmonology, Moscow, Russia
| | | | - S D Varfolomeev
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - E N Nikolaev
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
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38
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Larina IM, Pastushkova LK, Tiys ES, Kireev KS, Kononikhin AS, Starodubtseva NL, Popov IA, Custaud MA, Dobrokhotov IV, Nikolaev EN, Kolchanov NA, Ivanisenko VA. Permanent proteins in the urine of healthy humans during the Mars-500 experiment. J Bioinform Comput Biol 2015; 13:1540001. [PMID: 25572715 DOI: 10.1142/s0219720015400016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Urinary proteins serve as indicators of various conditions in human normal physiology and disease pathology. Using mass spectrometry proteome analysis, the permanent constituent of the urine was examined in the Mars-500 experiment (520 days isolation of healthy volunteers in a terrestrial complex with an autonomous life support system). Seven permanent proteins with predominant distribution in the liver and blood plasma as well as extracellular localization were identified. Analysis of the overrepresentation of the molecular functions and biological processes based on Gene Ontology revealed that the functional association among these proteins was low. The results showed that the identified proteins may be independent markers of the various conditions and processes in healthy humans and that they can be used as standards in determination of the concentration of other proteins in the urine.
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Affiliation(s)
- Irina M Larina
- Institute for Biomedical Problems - Russian Federation State, Scientific Research Center Russian Academy of Sciences, Moscow 123007, Russia , CaDyWEC International Laboratory, Angers Faculty of Medicine, 49045 Angers Cedex 01, France
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Pastushkova LK, Kononikhin AS, Tiys ES, Dobrokhotov IV, Ivanisenko VA, Nikolaev EN, Larina IM, Popov IA. [Urine proteome study for the evaluation of age dynamics in healthy men]. Adv Gerontol 2015; 28:694-700. [PMID: 28509457] [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] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigated the age dynamics of proteomic profile of urine in 52 healthy men aged 18 to 51 years. A special sample preparation was performed, followed by liquid chromatography-mass spectrometry. Liquid chromatography-mass spectrometry of the minor proteins was performed on a nano-HPLC Agilent 1100 system («Agilent Technologies Inc.», USA) in combination with a LTQ-FT Ultra mass spectrometer («Thermo Electron», Germany). A total of 259 proteins were identified. According to the TiGER database, a tissue origin was established for 141 proteins and identified 715 processes in which they participate. We found a significant positive correlation with age, the number of proteins (R=0,566; p-value=1,24E-05) and the weight of proteins (R=0,45; p value=8,17E-04). Identified 23 proteins were significantly more frequent in the urine of subjects with increasing age (p<0,05), and only one protein - RGSL, Regulator of G protein signaling protein-like (MW 125.69) - less frequently.
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Affiliation(s)
- L Kh Pastushkova
- Institute of Biomedical Problems, SSC RAS, Moscow, 123007, Russian Federation;
| | - A S Kononikhin
- Institute of Biomedical Problems, SSC RAS, Moscow, 123007, Russian Federation;
- N. M. Emanuel Institute of Biochemical Physics, SSC RAS, Moscow, 119334, Russian Federation
| | - E S Tiys
- Institute for Cytology and Genetics, RAS, Novosibirsk, 630090, Russian Federation
| | - I V Dobrokhotov
- Institute of Biomedical Problems, SSC RAS, Moscow, 123007, Russian Federation;
| | - V A Ivanisenko
- Institute for Cytology and Genetics, RAS, Novosibirsk, 630090, Russian Federation
| | - E N Nikolaev
- N. M. Emanuel Institute of Biochemical Physics, SSC RAS, Moscow, 119334, Russian Federation
- Institute for Energy Problems of Chemical Physics, SSC RAS, Moscow, 119334, Russian Federation
| | - I M Larina
- Institute of Biomedical Problems, SSC RAS, Moscow, 123007, Russian Federation;
| | - I A Popov
- N. M. Emanuel Institute of Biochemical Physics, SSC RAS, Moscow, 119334, Russian Federation
- Institute for Energy Problems of Chemical Physics, SSC RAS, Moscow, 119334, Russian Federation
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Feldman TB, Yakovleva MA, Arbukhanova PM, Borzenok SA, Kononikhin AS, Popov IA, Nikolaev EN, Ostrovsky MA. Changes in spectral properties and composition of lipofuscin fluorophores from human-retinal-pigment epithelium with age and pathology. Anal Bioanal Chem 2014; 407:1075-88. [PMID: 25471291 DOI: 10.1007/s00216-014-8353-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/16/2014] [Accepted: 11/17/2014] [Indexed: 10/24/2022]
Abstract
Fundus autofluorescence mostly originates from bisretinoid fluorophores in lipofuscin granules, which accumulate in retinal-pigment-epithelium cells with age. The dynamics of accumulation, photo-oxidation, and photodegradation of bisretinoids during aging or in the presence of pathology have been insufficiently investigated. Changes in spectral properties and composition of human lipofuscin-granule fluorophores with age and pathology have now been investigated by a high-performance liquid chromatography method using spectrophotometric and fluorescent detectors connected in series. It was found that: (i) N-retinylidene-N-retinylethanolamine (A2E) fluorescence intensity is not predominant in the chloroform extract of human-cadaver-eye retinal pigment epithelium studied; bisretinoid photo-oxidation and photodegradation products have much higher fluorescent properties; (ii) the relative emission maximum in the fluorescence spectrum of suspended retinal-pigment-epithelium cells obtained from an individual human-cadaver eye without pathology is irrespective of donor age and falls within the range 575 ± 15 nm; in two cadaver eyes with signs of age-related macular degeneration, emission maxima were shifted by 23-36 nm towards the shortwave region; and (iii) the ratio of bisretinoid photo-oxidation and photodegradation products to unoxidized bisretinoids in the chloroform extract of cadaver-eye retinal pigment epithelium increases with donor age, from 0.69 ± 0.03 to 1.32 ± 0.04. The differences in fluorescence properties between chloroform extracts obtained from cadaver eyes with and without signs of age-related macular degeneration could be used to increase the potential of fundus autofluorescence imaging as a noninvasive diagnostic method.
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Affiliation(s)
- Tatiana B Feldman
- Department of Molecular Physiology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory1, Moscow, 119991, Russia,
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Kadry B, Press CD, Alosh H, Opper IM, Orsini J, Popov IA, Brodsky JB, Macario A. Obesity increases operating room times in patients undergoing primary hip arthroplasty: a retrospective cohort analysis. PeerJ 2014; 2:e530. [PMID: 25210656 PMCID: PMC4157296 DOI: 10.7717/peerj.530] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/30/2014] [Indexed: 12/29/2022] Open
Abstract
Background. Obesity impacts utilization of healthcare resources. The goal of this study was to measure the relationship between increasing body mass index (BMI) in patients undergoing total hip arthroplasty (THA) with different components of operating room (OR) time. Methods. The Stanford Translational Research Integrated Database Environment (STRIDE) was utilized to identify all ASA PS 2 or 3 patients who underwent primary THA at Stanford Medical Center from February 1, 2008 through January 1, 2013. Patients were divided into five groups based on the BMI weight classification. Regression analysis was used to quantify relationships between BMI and the different components of total OR time. Results. 1,332 patients were included in the study. There were no statistically significant differences in age, gender, height, and ASA PS classification between the BMI groups. Normal-weight patients had a total OR time of 138.9 min compared 167.9 min (P < 0.001) for morbidly obese patients. At a BMI > 35 kg/m2 each incremental BMI unit increase was associated with greater incremental total OR time increases. Conclusion. Morbidly obese patients required significantly more total OR time than normal-weight patients undergoing a THA procedure. This increase in time is relevant when scheduling obese patients for surgery and has an important impact on health resource utilization.
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Affiliation(s)
- Bassam Kadry
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University Medical Center , Stanford, CA , USA
| | - Christopher D Press
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University Medical Center , Stanford, CA , USA
| | - Hassan Alosh
- Department of Orthopaedic Surgery, Hospital of the University of Pennsylvania , Silverstein, Philadelphia, PA , USA
| | - Isaac M Opper
- Stanford University Economics Department , Stanford, CA , USA
| | - Joe Orsini
- Stanford University Economics Department , Stanford, CA , USA
| | - Igor A Popov
- Stanford University Economics Department , Stanford, CA , USA
| | - Jay B Brodsky
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University Medical Center , Stanford, CA , USA
| | - Alex Macario
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University Medical Center , Stanford, CA , USA
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Popov IA, Indeĭkina MI, Pekov SI, Starodybtseva NL, Kononikhin AS, Nikolaeva MI, Kukaev EN, Kostiukevich II, Kozin SA, Makarov AA, Nikolaev EN. [Estimation of phosphorilation level of amyloid beta, extracted from human blood plasma. Ultra high resolution mass spectrometry]. Mol Biol (Mosk) 2014; 48:696-704. [PMID: 25842854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently it has been shown that phosphorylation of the Ser8 residue in amyloid-beta (pS8-Abeta) is tightly involved in the pathogenesis ofAlzheimer's disease. Since this modification occurs in the key metal-binding domain of amyloid-beta, and thus should seriously affect the interaction of pS8-Abeta with zinc ions, this isoform might be a potential precursor of pathogenic oligomeric forms of amyloid beta. Hence the level of pS8-Abeta in human biological fluids (such as blood, urine, cerebral spinal fluid) might resemble the different stages of the pathogenesis of Alzhe- imer's disease. The aim of this workwas to develop a prototype of an analytical method for quantitative determination of the level of pS8-Abeta isoform in binary mixtures with native amyloid-beta in order to further use it to determine the levels of phosphorylated amyloid-beta in blood plasma samples of patients with Alzheimer's disease.
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Perminova IV, Dubinenkov IV, Kononikhin AS, Konstantinov AI, Zherebker AY, Andzhushev MA, Lebedev VA, Bulygina E, Holmes RM, Kostyukevich YI, Popov IA, Nikolaev EN. Molecular mapping of sorbent selectivities with respect to isolation of Arctic dissolved organic matter as measured by Fourier transform mass spectrometry. Environ Sci Technol 2014; 48:7461-7468. [PMID: 24896646 DOI: 10.1021/es5015423] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The objectives of this study were to identify molecular features characteristic to arctic DOM from the Kolyma River basin and to elucidate structural imprints induced by a choice of the sorption technique. To achieve this goal, DOM was isolated from the Kolyma River basin with a use of three nonionic sorbents: Amberlite XAD-8 resin, PPL- and C18 - SPE cartridges, and one anion exchanging resin-diethylaminoethyl (DEAE) -cellulose. The structural studies were conducted with a use of electrospray ionization Fourier Transform Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry and liquid state (1)H NMR spectroscopy. The DOM isolates obtained with a use of PPL and C18 cartridges were characterized with higher content of aliphatic compounds as compared to XAD-8 and DEAE-isolates. In total, for all arctic DOM isolates we observed predominance of hydrogen saturated compounds with high H/C values of identified formulas from FT-ICR MS data. (1)H NMR spectroscopy studies have confirmed this trend and revealed high contribution of alkyl-chain protons into the spectral density of the arctic DOM reaching 43% for PPL isolates.
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Affiliation(s)
- Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 1-3, 119991 Moscow, Russia
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Popov IA, Nagornov K, Vladimirov GN, Kostyukevich YI, Nikolaev EN. Twelve million resolving power on 4.7 T Fourier transform ion cyclotron resonance instrument with dynamically harmonized cell--observation of fine structure in peptide mass spectra. J Am Soc Mass Spectrom 2014; 25:790-799. [PMID: 24604470 DOI: 10.1007/s13361-014-0846-7] [Citation(s) in RCA: 12] [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] [Received: 10/08/2013] [Revised: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.
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Affiliation(s)
- Igor A Popov
- Talrose Institute for Energy Problems of Chemical Physics of Russian Academy of Sciences, Moscow, Russia
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Terterov I, Vyatkina K, Kononikhin AS, Boitsov V, Vyazmin S, Popov IA, Nikolaev EN, Pevzner P, Dubina M. Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms. Rapid Commun Mass Spectrom 2014; 28:33-41. [PMID: 24285388 DOI: 10.1002/rcm.6757] [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] [Received: 08/06/2013] [Revised: 09/24/2013] [Accepted: 10/04/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Peptides and proteins are among the most important components of living systems. Different attempts have been made to experimentally model the formation of peptides from amino acid monomers in investigation of the origin of life. Detailed characterization of peptides formed under various conditions in such reactions is very important for understanding processes of abiogenic peptide formation. METHODS We used liquid chromatography coupled with tandem mass spectrometry (MS/MS) for an accurate study of homo-peptides formed in a model reaction: glutamic acid oligomerization catalyzed by 1,1'-carbonyldiimidazole in aqueous solution with 1 M of sodium or potassium chloride and without any salts. We used de novo sequencing software for peptide identification. In addition we propose an approach that uses more spectral information for de novo sequencing then standard methods. RESULTS Peptides up to 9 amino acids long were found in the experiments with KCl, while in experiments with NaCl and without salts only peptides of up to 7 amino acids were detected. Due to high salt concentrations in samples a high number of singly charged peptide ions with up to 4 substitutions of hydrogen atoms by sodium or potassium atoms were observed. De novo sequencing software provided correct identifications even for peptide ions with substitutions. CONCLUSIONS Multiple substitutions of hydrogen by alkali metal atoms in peptide ions strongly change their fragmentation patterns. Proposed approach for de novo sequencing was found very effective, even for ions with substitutions. So, it may be useful in more complicated cases like sequencing abiogenic peptides consisting of different amino acids.
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Affiliation(s)
- Ivan Terterov
- St. Petersburg Academic University Nanotechnology Research and Education Center RAS, 8/3 Khlopina st., St. Petersburg, 194021, Russia
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Pastushkova LK, Kireev KS, Kononikhin AS, Tiys ES, Popov IA, Dobrokhotov IV, Custaud MA, Ivanisenko VA, Kolchanov NA, Nikolaev EN, Pochuev VI, Larina IM. [Permanent proteins in healthy human's urine in the experiment with 520-day isolation]. Aviakosm Ekolog Med 2014; 48:48-54. [PMID: 25033613] [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: 06/03/2023]
Abstract
Purpose of the study was to track permanent proteins of urine proteome in the 520-day isolation experiment at the IBMP Ground-Based Test Facility with controlled environmental parameters. Object of the investigation was urine sampled from 6 normal male subjects at the age of 25 to 37 years. Second morning aliquots were gathered during baseline data collection, on days 50, 93, 124, 153, 180, 251, 274, 303, 330, 371, 400 and 427 of isolation, and in 7 days after its completion. Samples were subject to chromatography-mass spectrometry; results were analyzed with the help of bioinformatics resources. The following 7 permanent proteins were observed in urine over the entire length of the investigation: epidermal growth factor, polymer immunoglobulin receptor, plasma serine protease inhibitor, protein AMBP, keratin, type II cytoskeletal 1, collagen alpha-1 (vi) chain, serum albumin.
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Kulikova AA, Tsvetkov PO, Indeykina MI, Popov IA, Zhokhov SS, Golovin AV, Polshakov VI, Kozin SA, Nudler E, Makarov AA. Phosphorylation of Ser8 promotes zinc-induced dimerization of the amyloid-β metal-binding domain. ACTA ACUST UNITED AC 2014; 10:2590-6. [DOI: 10.1039/c4mb00332b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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
Phosphorylation of Ser8 leads to the formation of a new Zn2+ binding site and promotes zinc-induced dimerization of Aβ(1–16).
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Affiliation(s)
- Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
| | - Philipp O. Tsvetkov
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
| | - Maria I. Indeykina
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
- Emanuel Institute of Biochemical Physics
- Russian Academy of Sciences
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics
- Russian Academy of Sciences
- 119334 Moscow, Russia
| | - Sergey S. Zhokhov
- Faculty of Fundamental Medicine
- M.V. Lomonosov Moscow State University
- 119191 Moscow, Russia
| | - Andrey V. Golovin
- Bioengineering and Bioinformatics Department
- M.V. Lomonosov Moscow State University
- 119991 Moscow, Russia
| | - Vladimir I. Polshakov
- Faculty of Fundamental Medicine
- M.V. Lomonosov Moscow State University
- 119191 Moscow, Russia
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
- Orekhovich Institute of Biomedical Chemistry
- Russian Academy of Medical Sciences
| | - Evgeny Nudler
- Howard Hughes Medical Institute
- New York University School of Medicine
- New York, USA
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology
- Russian Academy of Sciences
- 119991 Moscow, Russia
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Pastushkova LK, Valeeva OA, Kononikhin AS, Nikolaev EN, Larina IM, Dobrokhotov IV, Popov IA, Pochuev VI, Kireev KS. Changes of protein profile of human urine after long-term orbital flights. Bull Exp Biol Med 2013; 156:201-4. [PMID: 24319748 DOI: 10.1007/s10517-013-2310-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We analyzed protein profile of urine samples obtained from 7 Russian cosmonauts (age 35-51 years), participants of space flights on the International Space Station lasting for 169-199 days. Gradient chromatography with linear increase of eluent proportion was carried out in a system consisting of an Agilent 1100 chromatograph (Agilent Technologies Inc.) and a hybrid mass-spectrometer LTQ-FT Ultra (Thermo). The obtained results help to understand changes in the human body induced by space flight factors.
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Affiliation(s)
- L Kh Pastushkova
- State Scientific Center of the Russian Federation Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia; N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow; Yu. A. Gagarin Research and Test Cosmonaut Training Center, Zvezdnyi Gorodok, Moscow Region; Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
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Popov IA, Starodubtseva NL, Indeĭkina MI, Kostiukevich II, Kononikhin AS, Nikolaeva MI, Kukaev EN, Kozin SA, Makarov AA, Nikolaev EN. [Identification of transthyretin posttranslational modifications 1n human blood using mass-spectrometric methods]. Mol Biol (Mosk) 2013; 47:1011-1019. [PMID: 25509863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Transthyretin, one of the major plasma proteins, has a number of posttranslational modifications and mutations, some of which are associated with the development of severe diseases, for instance, familial amyloid neuropathy and Alzheimer's disease. In order to investigate the role of modified forms in the development of these diseases a complex analytical platform, based on two mass-spectrometric approaches (bottom-up and op-down) has been developed. The high efficiency of this method was shown using 10 plasma samples obtained from patients with Alzheimer's disease and healthy individuals.
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Pastushkova LK, Kireev KS, Kononikhin AS, Tiĭs ES, Popov IA, Dobrokhotov IV, Ivanisenko VA, Noskov BV, Larina IM, Nikolaev EN. [Detection of renal and urinary tract proteins in the urine before and after space flight]. Fiziol Cheloveka 2013; 39:99-104. [PMID: 25509877] [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: 06/04/2023]
Abstract
The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques to obtain data in physiological condition and after six months space flights. It was shown that after long duration space flights in cosmonaut's urine reveals specific minor proteins which can be identified as proteins came from kidney and urinary tract.
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