1
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Keating MF, Wolfe CA, Liebenberg K, Montgomery A, Porcari AM, Fleming ND, Makarov A, Eberlin LS. Data Acquisition and Intraoperative Tissue Analysis on a Mobile, Battery-Operated, Orbitrap Mass Spectrometer. Anal Chem 2024. [PMID: 38739527 DOI: 10.1021/acs.analchem.4c00722] [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: 05/16/2024]
Abstract
Mass spectrometry has been increasingly explored in intraoperative studies as a potential technology to help guide surgical decision making. Yet, intraoperative experiments using high-performance mass spectrometry instrumentation present a unique set of operational challenges. For example, standard operating rooms are often not equipped with the electrical requirements to power a commercial mass spectrometer and are not designed to accommodate their permanent installation. These obstacles can impact progress and patient enrollment in intraoperative clinical studies because implementation of MS instrumentation becomes limited to specific operating rooms that have the required electrical connections and space. To expand our intraoperative clinical studies using the MasSpec Pen technology, we explored the feasibility of transporting and acquiring data on Orbitrap mass spectrometers operating on battery power in hospital buildings. We evaluated the effect of instrument movement including acceleration and rotational speeds on signal stability and mass accuracy by acquiring data using direct infusion electrospray ionization. Data were acquired while rolling the systems in/out of operating rooms and while descending/ascending a freight elevator. Despite these movements and operating the instrument on battery power, the relative standard deviation of the total ion current was <5% and the magnitude of the mass error relative to the internal calibrant never exceeded 5.06 ppm. We further evaluated the feasibility of performing intraoperative MasSpec Pen analysis while operating the Orbitrap mass spectrometer on battery power during an ovarian cancer surgery. We observed that the rich and tissue-specific molecular profile commonly detected from ovarian tissues was conserved when running on battery power. Together, these results demonstrate that Orbitrap mass spectrometers can be operated and acquire data on battery power while in motion and in rotation without losses in signal stability or mass accuracy. Furthermore, Orbitrap mass spectrometers can be used in conjunction to the MasSpec Pen while on battery power for intraoperative tissue analysis.
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Affiliation(s)
- Michael F Keating
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Charles A Wolfe
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Keziah Liebenberg
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ashley Montgomery
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Andreia M Porcari
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
- MS4Life Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, Universidade São Francisco, Bragança Paulista, SP 12916-900, Brazil
| | - Nicole D Fleming
- Department of Surgery, MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | - Livia S Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
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2
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Lyutvinskiy Y, Nagornov KO, Kozhinov AN, Gasilova N, Menin L, Meng Z, Zhang X, Saei AA, Fu T, Chamot-Rooke J, Tsybin YO, Makarov A, Zubarev RA. Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak. J Am Soc Mass Spectrom 2024; 35:902-911. [PMID: 38609335 PMCID: PMC11066971 DOI: 10.1021/jasms.3c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z starting from z = 1 and color coding z in m/z spectra. CHARDA combines the analysis of ion signal decay rates in the time-domain data (transients) in Fourier transform (FT) MS with the interrogation of mass defects (fractional mass) of biopolymers. Being applied to individual isotopic peaks in a complex protein tandem (MS/MS) data set, CHARDA aids peptide mass spectra interpretation by facilitating charge-state deconvolution of large ionic species in crowded regions, estimating z even in the absence of an isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust, and consistent with conventional FTMS and FTMS/MS data acquisition procedures. An effective charge-state resolution Rz ≥ 6 is obtained with the potential for further improvements.
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Affiliation(s)
- Yaroslav Lyutvinskiy
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | | | | | - Natalia Gasilova
- Ecole
Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laure Menin
- Ecole
Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Zhaowei Meng
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Xuepei Zhang
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Amir Ata Saei
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- Department
of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Centre for
Translational Microbiome Research, Department of Microbiology, Tumor
and Cell Biology, Karolinska Institutet, Stockholm 17165, Sweden
| | | | | | | | | | - Roman A. Zubarev
- Division
of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- Department
of Pharmacological & Technological Chemistry, I.M., Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- The National Medical Research
Center for Endocrinology, 115478 Moscow, Russia
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3
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Serrano LR, Peters-Clarke TM, Arrey TN, Damoc E, Robinson ML, Lancaster NM, Shishkova E, Moss C, Pashkova A, Sinitcyn P, Brademan DR, Quarmby ST, Peterson AC, Zeller M, Hermanson D, Stewart H, Hock C, Makarov A, Zabrouskov V, Coon JJ. The One Hour Human Proteome. Mol Cell Proteomics 2024; 23:100760. [PMID: 38579929 DOI: 10.1016/j.mcpro.2024.100760] [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: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
We describe deep analysis of the human proteome in less than 1 h. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, and data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high tandem mass spectrometry acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data-independent acquisition or data-dependent acquisition modes of operation. The fast-switching capabilities of the new quadrupole complement the sensitivity and fast ion scanning of the Astral analyzer to enable narrow-bin data-independent analysis methods. Over a 30-min active chromatographic method consuming a total analysis time of 56 min, the Q-Orbitrap-Astral hybrid MS collects an average of 4319 MS1 scans and 438,062 tandem mass spectrometry scans per run, producing 235,916 peptide sequences (1% false discovery rate). On average, each 30-min analysis achieved detection of 10,411 protein groups (1% false discovery rate). We conclude, with these results and alongside other recent reports, that the 1-h human proteome is within reach.
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Affiliation(s)
- Lia R Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Eugen Damoc
- Thermo Fisher Scientific GmbH, Bremen, Germany
| | - Margaret Lea Robinson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah M Lancaster
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Corinne Moss
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Pavel Sinitcyn
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | | | | | | | | | | | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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4
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Stewart H, Grinfeld D, Petzoldt J, Hagedorn B, Skoblin M, Makarov A, Hock C. Crowd control of ions in the Astral analyzer. J Mass Spectrom 2024; 59:e5006. [PMID: 38501497 DOI: 10.1002/jms.5006] [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] [Received: 12/27/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/20/2024]
Abstract
Space charge effects are the Achilles' heel of all high-resolution ion optical devices. In time-of-flight mass analyzers, these may manifest as reduction of resolving power, mass measurement shift, peak coalescence, and/or transmission losses, while highly sensitive modern ion sources and injection devices ensure that such limits are easily exceeded. Space charge effects have been investigated, by experiment and simulation study, for the astral multi-reflection analyzer, incorporating ion focusing via a pair of converging ion mirrors, and fed by a pulsed extraction ion trap. Major factors were identified as the resonant effect between ~103 ions of similar m/z in-flight and the expansion of trapped packets of ~104-5 ions prior to extraction. Optimum operation and compensated ion mirror calibration strategies were then generated and described based on these findings.
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5
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Ray S, Arévalo R, Southard A, Willhite L, Bardyn A, Ni Z, Danell R, Grubisic A, Gundersen C, Llano J, Yu A, Fahey M, Hernandez E, Graham J, Lee J, Ersahin A, Briois C, Thirkell L, Colin F, Makarov A. Characterization of Regolith And Trace Economic Resources (CRATER): An Orbitrap-based laser desorption mass spectrometry instrument for in situ exploration of the Moon. Rapid Commun Mass Spectrom 2024; 38:e9657. [PMID: 38342682 DOI: 10.1002/rcm.9657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 02/13/2024]
Abstract
RATIONALE Characterization of Regolith And Trace Economic Resources (CRATER), an Orbitrap™-based laser desorption mass spectrometry instrument designed to conduct high-precision, spatially resolved analyses of planetary materials, is capable of answering outstanding science questions about the Moon's formation and the subsequent processes that have modified its (sub)surface. METHODS Here, we describe the baseline design of the CRATER flight model, which requires <20 000 cm3 volume, <10 kg mass, and <60 W peak power. The analytical capabilities and performance metrics of a prototype that meets the full functionality of the flight model are demonstrated. RESULTS The instrument comprises a high-power, solid-state, pulsed ultraviolet (213 nm) laser source to ablate the surface of the lunar sample, a custom ion optical interface to accelerate and collimate the ions produced at the ablation site, and an Orbitrap mass analyzer capable of discriminating competing isobars via ultrahigh mass resolution and high mass accuracy. The CRATER instrument can measure elemental and isotopic abundances and characterize the organic content of lunar surface samples, as well as identify economically valuable resources for future exploration. CONCLUSION An engineering test unit of the flight model is currently in development to serve as a pathfinder for near-term mission opportunities.
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Affiliation(s)
- Soumya Ray
- University of Maryland, College Park, Maryland, USA
| | | | | | | | - Anais Bardyn
- University of Maryland, College Park, Maryland, USA
| | - Ziqin Ni
- University of Maryland, College Park, Maryland, USA
| | - Ryan Danell
- Danell Consulting, Winterville, North Carolina, USA
| | | | | | | | - Anthony Yu
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Molly Fahey
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | | | - Jacob Graham
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Jane Lee
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Akif Ersahin
- MAE Aerospace, South Glastonbury, Connecticut, USA
| | - Christelle Briois
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | - Laurent Thirkell
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | - Fabrice Colin
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
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6
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. Sci Adv 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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7
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Steigerwald S, Sinha A, Fort KL, Zeng WF, Niu L, Wichmann C, Kreutzmann A, Mourad D, Aizikov K, Grinfeld D, Makarov A, Mann M, Meier F. Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. Mol Cell Proteomics 2024; 23:100713. [PMID: 38184013 PMCID: PMC10851225 DOI: 10.1016/j.mcpro.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
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Affiliation(s)
- Sophia Steigerwald
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (GmbH), Bremen, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lili Niu
- Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christoph Wichmann
- Department Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | | | | | | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Department Clinical Proteomics, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Florian Meier
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Functional Proteomics, Jena University Hospital, Jena, Germany.
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8
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Guzman UH, Martinez-Val A, Ye Z, Damoc E, Arrey TN, Pashkova A, Renuse S, Denisov E, Petzoldt J, Peterson AC, Harking F, Østergaard O, Rydbirk R, Aznar S, Stewart H, Xuan Y, Hermanson D, Horning S, Hock C, Makarov A, Zabrouskov V, Olsen JV. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nat Biotechnol 2024:10.1038/s41587-023-02099-7. [PMID: 38302753 DOI: 10.1038/s41587-023-02099-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th isolation windows, dissolving the differences between data-dependent and -independent methods. This is achieved by pairing a quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Eugen Damoc
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | - Anna Pashkova
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | - Florian Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Rydbirk
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susana Aznar
- Centre for Neuroscience and Stereology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Yue Xuan
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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9
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Stewart H, Grinfeld D, Wagner A, Kholomeev A, Biel M, Giannakopulos A, Makarov A, Hock C. A Conjoined Rectilinear Collision Cell and Pulsed Extraction Ion Trap with Auxiliary DC Electrodes. J Am Soc Mass Spectrom 2024; 35:74-81. [PMID: 37925680 PMCID: PMC10767742 DOI: 10.1021/jasms.3c00311] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Ion traps are routinely directly coupled to mass analyzers, where they serve to suitably cool and shape an ion population prior to pulsed extraction into the analyzer proper. Such devices benefit from high duty cycle and transmission but suffer slow ion processing times caused by a compromise in the buffer gas pressure range that suitably dampens the ion kinetic energy without causing excessive scatter during extraction or within the analyzer. A rectilinear RF quadrupole ion trap has been characterized, conjoining a pressurized collision region with a pumped extraction region, and an unbroken RF interface for seamless ion transfer between them. Auxiliary electrodes mounted between the RF electrodes provide DC voltage gradients that serve to both guide ions through the device and position them at the extraction slot. The influence of the auxiliary DC upon the trapping RF field was measured, and suitable parameters were defined. A mode of operation was developed that allowed parallel processing of ions in both regions, enabling a repetition rate of 200 Hz when the device was coupled to a high-resolution accurate-mass analyzer.
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Affiliation(s)
- Hamish Stewart
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Dmitry Grinfeld
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Alexander Wagner
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Matthias Biel
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Christian Hock
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
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10
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Tyaginov S, Bury E, Grill A, Yu Z, Makarov A, De Keersgieter A, Vexler M, Vandemaele M, Wang R, Spessot A, Chasin A, Kaczer B. Compact Physics Hot-Carrier Degradation Model Valid over a Wide Bias Range. Micromachines (Basel) 2023; 14:2018. [PMID: 38004876 PMCID: PMC10673430 DOI: 10.3390/mi14112018] [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] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
We develop a compact physics model for hot-carrier degradation (HCD) that is valid over a wide range of gate and drain voltages (Vgs and Vds, respectively). Special attention is paid to the contribution of secondary carriers (generated by impact ionization) to HCD, which was shown to be significant under stress conditions with low Vgs and relatively high Vds. Implementation of this contribution is based on refined modeling of carrier transport for both primary and secondary carriers. To validate the model, we employ foundry-quality n-channel transistors and a broad range of stress voltages {Vgs,Vds}.
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Affiliation(s)
- Stanislav Tyaginov
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Erik Bury
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Alexander Grill
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Zhuoqing Yu
- Institute of Microelectronics, Peking University, Beijing 100871, China; (Z.Y.); (R.W.)
| | - Alexander Makarov
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - An De Keersgieter
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Mikhail Vexler
- A.F. Ioffe Institute, Polytechnicheskaya 26, 194021 St.-Petersburg, Russia;
| | - Michiel Vandemaele
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Runsheng Wang
- Institute of Microelectronics, Peking University, Beijing 100871, China; (Z.Y.); (R.W.)
| | - Alessio Spessot
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Adrian Chasin
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
| | - Ben Kaczer
- Imec, Kapeldreef 75, 3001 Leuven, Belgium; (E.B.); (A.G.); (A.M.); (A.D.K.); (A.S.); (A.C.); (B.K.)
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11
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Smyrnakis A, Levin N, Kosmopoulou M, Jha A, Fort K, Makarov A, Papanastasiou D, Mohammed S. Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins. Anal Chem 2023; 95:12039-12046. [PMID: 37534599 PMCID: PMC10433246 DOI: 10.1021/acs.analchem.3c01899] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides.
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Affiliation(s)
- Athanasios Smyrnakis
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Nikita Levin
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Pharmacology, University of Oxford, OX1 3QT Oxford, U.K.
| | - Kyle Fort
- Thermo
Fisher Scientific, 28199 Bremen, Germany
| | | | - Dimitris Papanastasiou
- Fasmatech
Science & Technology, Lefkippos Tech. Park, NCSR Demokritos, 15341 Agia Paraskevi, Greece
| | - Shabaz Mohammed
- Rosalind
Franklin Institute, Harwell Campus, OX11 0QX Didcot, U.K.
- Department
of Biochemistry, University of Oxford, OX1 3QU Oxford, U.K.
- Department
of Chemistry, University of Oxford, OX1 3TA Oxford, U.K.
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12
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Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun 2023; 14:3599. [PMID: 37328457 PMCID: PMC10276052 DOI: 10.1038/s41467-023-39347-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
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Affiliation(s)
- Ana Martínez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kyle Fort
- Thermo Fisher Scientific, Bremen, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Yue Xuan
- Thermo Fisher Scientific, Bremen, Germany.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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13
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Ni Z, Arevalo R, Bardyn A, Willhite L, Ray S, Southard A, Danell R, Graham J, Li X, Chou L, Briois C, Thirkell L, Makarov A, Brinckerhoff W, Eigenbrode J, Junge K, Nunn BL. Detection of Short Peptides as Putative Biosignatures of Psychrophiles via Laser Desorption Mass Spectrometry. Astrobiology 2023; 23:657-669. [PMID: 37134219 DOI: 10.1089/ast.2022.0138] [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: 05/05/2023]
Abstract
Studies of psychrophilic life on Earth provide chemical clues as to how extraterrestrial life could maintain viability in cryogenic environments. If living systems in ocean worlds (e.g., Enceladus) share a similar set of 3-mer and 4-mer peptides to the psychrophile Colwellia psychrerythraea on Earth, spaceflight technologies and analytical methods need to be developed to detect and sequence these putative biosignatures. We demonstrate that laser desorption mass spectrometry, as implemented by the CORALS spaceflight prototype instrument, enables the detection of protonated peptides, their dimers, and metal adducts. The addition of silicon nanoparticles promotes the ionization efficiency, improves mass resolving power and mass accuracies via reduction of metastable decay, and facilitates peptide de novo sequencing. The CORALS instrument, which integrates a pulsed UV laser source and an Orbitrap™ mass analyzer capable of ultrahigh mass resolving powers and mass accuracies, represents an emerging technology for planetary exploration and a pathfinder for advanced technique development for astrobiological objectives. Teaser: Current spaceflight prototype instrument proposed to visit ocean worlds can detect and sequence peptides that are found enriched in at least one strain of microbe surviving in subzero icy brines via silicon nanoparticle-assisted laser desorption analysis.
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Affiliation(s)
- Ziqin Ni
- University of Maryland, College Park, Maryland, USA
| | | | - Anais Bardyn
- University of Maryland, College Park, Maryland, USA
| | | | - Soumya Ray
- University of Maryland, College Park, Maryland, USA
| | | | - Ryan Danell
- Danell Consulting, Winterville, North Carolina, USA
| | - Jacob Graham
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Xiang Li
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Georgetown University, Washington, DC, USA
| | - Christelle Briois
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | - Laurent Thirkell
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace, Orléans, France
| | | | | | | | - Karen Junge
- University of Washington, Seattle, Washington, USA
| | - Brook L Nunn
- University of Washington, Seattle, Washington, USA
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14
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis. Anal Chem 2023; 95:7656-7664. [PMID: 37133913 DOI: 10.1021/acs.analchem.3c00594] [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: 05/04/2023]
Abstract
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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15
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Advancing Orbitrap Measurements of Collision Cross Sections to Multiple Species for Broad Applications. Anal Chem 2022; 94:15613-15620. [DOI: 10.1021/acs.analchem.2c02146] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Virginia K. James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | | | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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16
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Papanastasiou D, Kounadis D, Lekkas A, Orfanopoulos I, Mpozatzidis A, Smyrnakis A, Panagiotopoulos E, Kosmopoulou M, Reinhardt-Szyba M, Fort K, Makarov A, Zubarev RA. The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry. J Am Soc Mass Spectrom 2022; 33:1990-2007. [PMID: 36113052 PMCID: PMC9850925 DOI: 10.1021/jasms.2c00214] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.
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Affiliation(s)
- Dimitris Papanastasiou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Diamantis Kounadis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Alexandros Lekkas
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Ioannis Orfanopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Andreas Mpozatzidis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Athanasios Smyrnakis
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Elias Panagiotopoulos
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Mariangela Kosmopoulou
- Fasmatech
Science & Technology, TESPA Lefkippos, NCSR Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | | | - Kyle Fort
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo
Fisher Scientific, Hanna-Kunath-Straße
11, 28199 Bremen, Germany
| | - Roman A. Zubarev
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17165 Solna, Sweden
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17
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS Nexus 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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18
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Abstract
Introduction. A disadvantage of the ancestral method (la méthode ancestrale), which is widely used in the production of sparkling wine, is that it is difficult to control fermentation. We aimed to identify the optimal yeast race for obtaining high-quality young sparkling wines with varietal aroma without yeast tones.
Study objects and methods. Our study objects were base and young sparkling wines from Cabernet-Sauvignon prepared on various yeast races. Organic acids, sugars, and ethanol contents were determined by high performance liquid chromatography. Phenolic and coloring substances were measured by colorimetric method. Foaming properties were determined by air barbotage of a wine sample in a measuring cylinder; sparkling properties, by measuring the CO2 desorption rate; CO2 content, by volumetric method; viscosity, with a viscometer. Sensory evaluation was carried out according to standard methods.
Results and discussion. The wines produced on the Odesskiy Chernyi-SD13 yeast race received the highest tasting scores of 7.82 and 9.05 points for base wine and young sparkling wines, respectively. They contained larger amounts of phenolic substances (1103 mg/dm3) and coloring agents (275 mg/dm3) and had higher color intensity (1.614). The panelists rated them highly on their complex varietal aroma and harmonious, velvety flavor, as well as their foaming and sparkling properties. This yeast race ensured intensive fermentation of sugars and a great amount of bound CO2 (up to 24.93%).
Conclusion. The Odesskiy Chernyi-SD13 yeast race is optimal for making base and young sparkling wines by the bottle method. This technology can be used to produce high-quality sparkling wines in the crop year by large and small enterprises.
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Affiliation(s)
- Alexander Makarov
- All-Russian National Research Institute of Viticulture and Winemaking “Magarach” of RAS
| | - Igor Lutkov
- All-Russian National Research Institute of Viticulture and Winemaking “Magarach” of RAS
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19
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Korobov Y, Alwan H, Soboleva N, Makarov A, Lezhnin N, Shumyakov V, Antonov M, Deviatiarov M. Cavitation Resistance of WC-10Co4Cr and WC-20CrC-7Ni HVAF Coatings. J Therm Spray Technol 2021; 31:234-246. [PMID: 38624694 PMCID: PMC8360761 DOI: 10.1007/s11666-021-01242-7] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 04/17/2024]
Abstract
Machines operating in aqueous environments may be subjected to cavitation damage during operation. This study aims to evaluate the cavitation resistance of WC-10Co4Cr and WC-20CrC-7Ni coatings under cavitation erosion conditions with additional electrochemical effects. The coatings were deposited on AISI 1040 steel substrates using a high velocity air fuel thermal spray process. The microstructure of the coatings was observed by a scanning electron microscope, while their phase composition was analyzed using an energy-dispersive microanalysis system. In addition, the microhardness of the coatings and substrate was measured, and the surface topography of the eroded surface layers was observed using a 3D optical profilometer. The results revealed that the cavitation resistance of the WC-20CrC-7Ni coatings was better than that of the WC-10Co4Cr coatings. The observation of the structure and surface topography made it possible to identity the reasons for the differences between the cavitation resistance of both coatings: The WC-20CrC-7Ni coatings had a finer grain structure, lower pore density, and lower as-sprayed surface roughness. These differences, along with the presence of a high Cr and Ni content in the feedstock powder, that increased the coating corrosion resistance, contributed to improving the cavitation resistance and reducing the material loss of the WC-20CrC-7Ni coatings.
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Affiliation(s)
- Yu. Korobov
- M. N. Miheev Institute of Metal Physics, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
- Ural Federal University, Yekaterinburg, Russian Federation
| | - H. Alwan
- Ural Federal University, Yekaterinburg, Russian Federation
- University of Technology, Baghdad, Republic of Iraq
| | - N. Soboleva
- Ural Federal University, Yekaterinburg, Russian Federation
- Institute of Engineering Science, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - A. Makarov
- M. N. Miheev Institute of Metal Physics, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - N. Lezhnin
- M. N. Miheev Institute of Metal Physics, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - V. Shumyakov
- Ural Federal University, Yekaterinburg, Russian Federation
| | - M. Antonov
- Tallinn University of Technology, Tallinn, Estonia
| | - M. Deviatiarov
- Ural Welding Institute-Metallurgy, Yekaterinburg, Russian Federation
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20
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Vishnyakova P, Poltavets A, Karpulevich E, Maznina A, Vtorushina V, Mikhaleva L, Kananykhina E, Lokhonina A, Kovalchuk S, Makarov A, Elchaninov A, Sukhikh G, Fatkhudinov T. The response of two polar monocyte subsets to inflammation. Biomed Pharmacother 2021; 139:111614. [PMID: 33930675 DOI: 10.1016/j.biopha.2021.111614] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Macrophages are a central component of innate immunity that play an important role in the defense of the organism. Macrophages are highly plastic and are activated by interaction with other cells and environmental factors. In this work, we study the effect of lipopolysaccharide on macrophages derived from the two most polar (CD14+ and CD16+ monocytes) as well as the intermediate subset of blood monocytes from healthy donors and assess what happens to the subset most prone to polarization on the transcriptomic and proteomic level. It has been shown that, according to primary pro-inflammatory polarization markers, their cytokine profile, and their phagocytic activity, macrophages derived from CD14+ monocytes exhibit higher sensitivity to inducers of pro-inflammatory polarization. Flow cytometry analysis revealed increased levels of CD86, while secretome analysis demonstrated significant increase of pro-inflammatory and anti-inflammatory cytokines observed in CD14+-derived macrophages, as compared to CD16+-derived macrophages in conditioned media. Assessment of the transcriptome and proteome of CD14+-derived macrophages with further bioinformatic analysis identified the most significant differences after polarization towards the pro-inflammatory phenotype. Immune-, membrane-, IFN-γ-, cytokine-, and defense-associated pathways were found significantly prevalent, while downregulated pathways were represented by RNA binding-, housekeeping-, exocytosis-, intracellular transport-, peptide and amide metabolic-related signaling. This data could be useful for macrophage-based cell therapeutics of cancer, as it provides additional background for the manipulation of donor monocytes intended for back transplantation.
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Affiliation(s)
- P Vishnyakova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; Рeoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia.
| | - A Poltavets
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - E Karpulevich
- Ivannikov Institute for System Programming of the Russian Academy of Sciences, 109004 Moscow, Russia; Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - A Maznina
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - V Vtorushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - L Mikhaleva
- Scientific Research Institute of Human Morphology, 117418 Moscow, Russia
| | - E Kananykhina
- Scientific Research Institute of Human Morphology, 117418 Moscow, Russia
| | - A Lokhonina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; Рeoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - S Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - A Makarov
- Рeoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia; Scientific Research Institute of Human Morphology, 117418 Moscow, Russia
| | - A Elchaninov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia; Scientific Research Institute of Human Morphology, 117418 Moscow, Russia
| | - G Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - T Fatkhudinov
- Рeoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia; Scientific Research Institute of Human Morphology, 117418 Moscow, Russia
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Kösling P, Rüger CP, Schade J, Fort KL, Ehlert S, Irsig R, Kozhinov AN, Nagornov KO, Makarov A, Rigler M, Tsybin YO, Walte A, Zimmermann R. Vacuum Laser Photoionization inside the C-trap of an Orbitrap Mass Spectrometer: Resonance-Enhanced Multiphoton Ionization High-Resolution Mass Spectrometry. Anal Chem 2021; 93:9418-9427. [PMID: 34170684 DOI: 10.1021/acs.analchem.1c01018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
State-of-the-art mass spectrometry with ultraviolet (UV) photoionization is mostly limited to time-of-flight (ToF) mass spectrometers with 1000-10 000 m/Δm mass resolution. However, higher resolution and higher spectral dynamic range mass spectrometry may be indispensable in complex mixture characterization. Here, we present the concept, implementation, and initial evaluation of a compact ultrahigh-resolution mass spectrometer with gas-phase laser ionization. The concept is based on direct laser photoionization in the ion accumulation and ejection trap (C-trap) of an Orbitrap mass spectrometer. Resonance-enhanced multiphoton ionization (REMPI) using 266 nm UV pulses from a frequency-quadrupled Nd:YAG laser was applied for selective and efficient ionization of monocyclic and polycyclic aromatic hydrocarbons. The system is equipped with a gas inlet for volatile compounds and a heated gas chromatography coupling. The former can be employed for rapid system m/z-calibration and performance evaluation, whereas the latter enables analysis of semivolatile and higher-molecular-weight compounds. The capability to evaluate complex mixtures is demonstrated for selected petrochemical materials. In these experiments, several hundred to over a thousand compounds could be attributed with a root-mean-square mass error generally below 1 ppm and a mass resolution of over 140 000 at 200 m/z. Isobaric interferences could be resolved, and narrow mass splits, such as 3.4 mDa (SH4/C3), are determined. Single laser shots provided limits of detection in the 20-ppb range for p-xylene and 1,2,4-trimethylbenzene, similar to compact vacuum REMPI-ToF systems.
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Affiliation(s)
- Paul Kösling
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Julian Schade
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany
| | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Sven Ehlert
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Photonion GmbH, 19061 Schwerin, Germany
| | - Robert Irsig
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Photonion GmbH, 19061 Schwerin, Germany
| | | | | | | | | | | | | | - Ralf Zimmermann
- Joint Mass Spectrometry Centre (JMSC)/Chair of Analytical Chemistry, University of Rostock, 18059 Rostock, Germany.,Department Life, Light & Matter (LLM), University of Rostock, 18059 Rostock, Germany.,Joint Mass Spectrometry Centre, Cooperation Group "Comprehensive Molecular Analytics", Helmholtz Zentrum Muenchen, Neuherberg D-85764, Germany
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22
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Makarov A, Lutkov I, Shmigelskaya N, Maksimovskaia V, Sivochoub G. Using of autochthonous grape varieties in the production of sparkling wines. BIO Web Conf 2021. [DOI: 10.1051/bioconf/20213907001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to increase the production of original and recognizable sparkling wines, base wines from autochthonous grape varieties can be used for their preparation. Based on the studied basic and advanced physicochemical and organoleptic characteristics, it was concluded about the possibility of using autochthonous grape varieties - ‘Makhrovatchic’, ‘Tsimlyanskii Belyi’, ‘Tsimladar’, ‘Kefesiya’, ‘Kokur Krasnyi’ and ‘Chernyi Krymskii’ - for production of high-quality sparkling wines. The relationships of the phenolic complex components with the parameters of sparkling wines, characterizing their appearance, was established, so for white sparkling wines - mass concentration of polymeric forms of phenolic substances with yellowness index (r = 0.925); for red ones - mass concentration of monomeric forms of phenolic compounds and mass concentration of coloring agents with the index of color intensity r = 0.580 and r = 0.786, respectively; for white and red sparkling wines - mass concentration of polymeric forms of phenolic substances with a maximum foam volume (r = 0.628). It was also noted as a positive factor that all samples accumulated a sufficient amount of the bound CO2 (not less than 8% of the total bottle content.
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Russkikh N, Antonets D, Shtokalo D, Makarov A, Vyatkin Y, Zakharov A, Terentyev E. Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis. Bioinformatics 2020; 36:5076-5085. [PMID: 33026062 PMCID: PMC7755413 DOI: 10.1093/bioinformatics/btaa624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 04/06/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Motivation The transcriptomic data are being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are the data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the samples which we would like to control (gender, biological state, treatment, etc.) can be used as style components. Results The proposed style transfer solution is based on Conditional Variational Autoencoders, Y-Autoencoders and adversarial feature decomposition. To quantitatively measure the quality of the style transfer, neural network classifiers which predict the style and semantics after training on real expression were used. Comparison with several existing style-transfer based approaches shows that proposed model has the highest style prediction accuracy on all considered datasets while having comparable or the best semantics prediction accuracy. Availability and implementation https://github.com/NRshka/stvae-source. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nikolai Russkikh
- AcademGene LLC, Novosibirsk 630090, Russia.,Laboratory of Complex Systems Simulation, A.P.Ershov Institute of Informatics Systems SB RAS, Novosibirsk 630090, Russia
| | - Denis Antonets
- AcademGene LLC, Novosibirsk 630090, Russia.,Laboratory of Complex Systems Simulation, A.P.Ershov Institute of Informatics Systems SB RAS, Novosibirsk 630090, Russia.,Theoretical Department, Research Center of Virology and Biotechnology "Vector" Rospotrebnadzor, Koltsovo 630559, Russia
| | - Dmitry Shtokalo
- AcademGene LLC, Novosibirsk 630090, Russia.,Laboratory of Complex Systems Simulation, A.P.Ershov Institute of Informatics Systems SB RAS, Novosibirsk 630090, Russia.,Cancer Research Foundation, Moscow 109316, Russia
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Barykin E, Garifulina A, Adzhubei A, Shelukhina I, Kozin SA, Mitkevich V, Tsetlin V, Makarov A. Identification of α4β2 nAChR interaction site with Aβ
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and development of tetrapeptide capable of breaking this interaction. Alzheimers Dement 2020. [DOI: 10.1002/alz.040936] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Evgeny Barykin
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Alexandra Garifulina
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia
| | - Alexei Adzhubei
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Irina Shelukhina
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Victor Tsetlin
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia
| | - Alexander Makarov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
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Kozin SA, Lazarev V, Tsolaki M, Mikhailova E, Benken K, Shevtsov M, Nikotina A, Mitkevich V, Makarov A, Margulis B, Guzhova I. Extracellular complex of beta‐amyloid with glyceraldehyde‐3‐phosphate dehydrogenase contributes to neurodegeneration in Alzheimer’s disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.043347] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sergey A. Kozin
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Vladimir Lazarev
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
| | - Magda Tsolaki
- Aristotle University of Thessaloniki Thessaloniki Greece
| | - Elena Mikhailova
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
| | | | - Maxim Shevtsov
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
| | - Alina Nikotina
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Alexander Makarov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Boris Margulis
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
| | - Irina Guzhova
- Institute of Cytology of the Russian Academy of Sciences St. Petersburg Russia
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Semchenko A, Makarov A, Karpov I, Zharenkov M. Microscope-Assisted Coronary Artery Bypass Grafting: Technique and Results. Braz J Cardiovasc Surg 2020; 35:815-820. [PMID: 33118747 PMCID: PMC7598973 DOI: 10.21470/1678-9741-2019-0416] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The microscope-assisted coronary artery bypass grafting (CABG) is a special technique of direct myocardial revascularization by the operating microscope using special equipment and atraumatic sutures. This method allows to complete elimination of technical errors during the performance of distal anastomoses and can be used to improve the outcomes and quality of conventional technique of operations. This article focuses on a detailed description of the technique for performing a distal anastomosis using a microsurgical technique and an operating microscope. Immediate results of operations are also reported. The data obtained suggest that microscope-assisted CABG is a safe, effective and reproducible procedure.
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Affiliation(s)
- Andrey Semchenko
- Federal Center for Cardiovascular Surgery of Healthcare Ministry of the Russian Federation Khabarovsk Russia Federal Center for Cardiovascular Surgery of Healthcare Ministry of the Russian Federation, Khabarovsk, Russia
| | - Alexander Makarov
- Federal Center for Cardiovascular Surgery of Healthcare Ministry of the Russian Federation Khabarovsk Russia Federal Center for Cardiovascular Surgery of Healthcare Ministry of the Russian Federation, Khabarovsk, Russia
| | - Ilya Karpov
- Far Eastern State Medical University of Healthcare Ministry of the Russian Federation Khabarovsk Russia Far Eastern State Medical University of Healthcare Ministry of the Russian Federation, Khabarovsk, Russia
| | - Mihail Zharenkov
- Far Eastern State Medical University of Healthcare Ministry of the Russian Federation Khabarovsk Russia Far Eastern State Medical University of Healthcare Ministry of the Russian Federation, Khabarovsk, Russia
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Makarov A, Roussel P, Bury E, Vandemaele M, Spessot A, Linten D, Kaczer B, Tyaginov S. Correlated Time-0 and Hot-Carrier Stress Induced FinFET Parameter Variabilities: Modeling Approach. Micromachines (Basel) 2020; 11:mi11070657. [PMID: 32630139 PMCID: PMC7407495 DOI: 10.3390/mi11070657] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/23/2022]
Abstract
We identify correlation between the drain currents in pristine n-channel FinFET transistors and changes in time-0 currents induced by hot-carrier stress. To achieve this goal, we employ our statistical simulation model for hot-carrier degradation (HCD), which considers the effect of random dopants (RDs) on HCD. For this analysis we generate a set of 200 device instantiations where each of them has its own unique configuration of RDs. For all “samples” in this ensemble we calculate time-0 currents (i.e., currents in undamaged FinFETs) and then degradation characteristics such as changes in the linear drain current and device lifetimes. The robust correlation analysis allows us to identify correlation between transistor lifetimes and drain currents in unstressed devices, which implies that FinFETs with initially higher currents degrade faster, i.e., have more prominent linear drain current changes and shorter lifetimes. Another important result is that although at stress conditions the distribution of drain currents becomes wider with stress time, in the operating regime drain current variability diminishes. Finally, we show that if random traps are also taken into account, all the obtained trends remain the same.
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Affiliation(s)
- Alexander Makarov
- Institute for Microelectronics, TU Wien, 1040 Vienna, Austria
- Correspondence: ; Tel.: +43-1-58801-36028
| | - Philippe Roussel
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
| | - Erik Bury
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
| | - Michiel Vandemaele
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
- Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium
| | - Alessio Spessot
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
| | - Dimitri Linten
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
| | - Ben Kaczer
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
| | - Stanislav Tyaginov
- Institute for Microelectronics, TU Wien, 1040 Vienna, Austria
- Imec, 3001 Leuven, Belgium; (P.R.); (E.B.); (M.V.); (A.S.); (D.L.); (B.K.); (S.T.)
- Ioffe Institute, 194021 St. Petersburg, Russia
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Mishchenko N, Svinar E, Makarov A. FEATURES OF PHYSICAL ADAPTATION OF FIRST-YЕAR UNIVERSITY STUDENTS TO AN URBANIZЕD ЕNVIRONMЕNT. hsm 2020. [DOI: 10.14529/hsm200102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Aim. The article is aimed at evaluating physiological adaptation (physical development, physical fitness and sickness rate) in first-year female university students not involved in sports to the urban conditions of the Kirov region. Materials and methods. Five hundred and thirty first-year female students not involved in sports (Vyatka State University, Kirov) participated in the study. Their physical development was estimated with the help of five anthropometric and eight physiometric parameters used for calculating 24 indices. To assess physical fitness, five types of tests were performed measuring general stamina, quickness, strength and other parameters. To evaluate the influence of urban environment, the participants were divided into three groups depending on the population of their home cities: “big city”, “small town”, “village”. Results. First-year female students, who used to live in a big city before entering the university, have smaller chest circumference at rest and at maximum inhalation/exhalation than the girls of the same height and weight, who used to live in small towns or villages. Urban environment influences physical fitness, which results in generally low stamina and strength typical for females living in Kirov. Conclusion. The results obtained show that the increase in urbanization puts pressure on the mechanisms of physiological adaptation in first-year female students who used to live in small towns and villages before entering the university.
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Bekker-Jensen DB, Martínez-Val A, Steigerwald S, Rüther P, Fort KL, Arrey TN, Harder A, Makarov A, Olsen JV. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Mol Cell Proteomics 2020; 19:716-729. [PMID: 32051234 PMCID: PMC7124470 DOI: 10.1074/mcp.tir119.001906] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [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: 12/11/2019] [Revised: 02/03/2020] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.
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Affiliation(s)
- Dorte B Bekker-Jensen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Ana Martínez-Val
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Sophia Steigerwald
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Patrick Rüther
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | | | | | | | | | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK.
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Salikhova D, Leonov G, Bukharova T, Kornienko Z, Bulatenko N, Efremova A, Makhnach O, Makarov A, Elchaninov A, Fathudinov T, Goldshtein D. Comparative impact analysis of neuronal and glial progenitors conditioned medium on cerebellar neurons under glutamate exitotoxicity. G&C 2019. [DOI: 10.23868/201912031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Affiliation(s)
- Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Str. 11, 28199, Bremen, Germany.
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Nolting D, Malek R, Makarov A. Ion traps in modern mass spectrometry. Mass Spectrom Rev 2019; 38:150-168. [PMID: 29084367 DOI: 10.1002/mas.21549] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
This review is devoted to trapping mass spectrometry wherein ions are confined by electromagnetic fields for prolonged periods of time within limited volume, with mass measurement taking place within the same volume. Three major types of trapping mass spectrometers are discussed, specifically radiofrequency ion trap, Fourier transform ion cyclotron resonance and Orbitrap. While these three branches are intricately interwoven with each other over their recent history, they also differ greatly in their fundamentals, roots and historical origin. This diversity is reflected also in the difference of viewpoints from which each of these directions is addressed in this review. Following the theme of the issue, we focus on developments mainly associated with the country of Germany but, at the same time, we use this review as an illustration of the rapidly increasing globalization of science and expanding multi-national collaborations.
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Arevalo R, Selliez L, Briois C, Carrasco N, Thirkell L, Cherville B, Colin F, Gaubicher B, Farcy B, Li X, Makarov A. An Orbitrap-based laser desorption/ablation mass spectrometer designed for spaceflight. Rapid Commun Mass Spectrom 2018; 32:1875-1886. [PMID: 30048021 DOI: 10.1002/rcm.8244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE The investigation of cryogenic planetary environments as potential harbors for extant life and/or contemporary sites of organic synthesis represents an emerging focal point in planetary exploration. Next generation instruments need to be capable of unambiguously determining elemental and/or molecular stoichiometry via highly accurate mass measurements and the separation of isobaric interferences. METHODS An Orbitrap™ analyzer adapted for spaceflight (referred to as the CosmOrbitrap), coupled with a commercial pulsed UV laser source (266 nm), was used to successfully characterize a variety of planetary analog samples via ultrahigh resolution laser desorption/ablation mass spectrometry. The materials analyzed in this study include: jarosite (a hydrous sulfate detected on Mars); magnesium sulfate (a potential component of the subsurface ocean on Europa); uracil (a nucleobase of RNA); and a variety of amino acids. RESULTS The instrument configuration tested here enables: measurement of major elements and organic molecules with ultrahigh mass resolution (m/Δm ≥ 120,000, FWHM); quantification of isotopic abundances with <1.0% (2σ) precision; and identification of highly accurate masses within 3.2 ppm of absolute values. The analysis of a residue of a dilute solution of amino acids demonstrates the capacity to detect twelve amino acids in positive ion mode at concentrations as low as ≤1 pmol/mm2 while maintaining mass resolution and accuracy requirements. CONCLUSIONS The CosmOrbitrap mass analyzer is highly sensitive and delivers mass resolution/accuracy unmatched by any instrument sent into orbit or launched into deep space. This prototype instrument, which maps to a spaceflight implementation, represents a mission-enabling technology capable of advancing planetary exploration for decades to come.
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Affiliation(s)
- Ricardo Arevalo
- Department of Geology, University of Maryland, College Park, MD, 20742, USA
| | - Laura Selliez
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
- Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), 78280, Guyancourt, France
| | - Christelle Briois
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
| | - Nathalie Carrasco
- Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), 78280, Guyancourt, France
| | - Laurent Thirkell
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
| | - Barnabé Cherville
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
| | - Fabrice Colin
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
| | - Bertrand Gaubicher
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR 7328 du CNRS, 45071, Orléans, France
| | - Benjamin Farcy
- Department of Geology, University of Maryland, College Park, MD, 20742, USA
| | - Xiang Li
- Center for Space Science & Technology, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
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Shaw JB, Malhan N, Vasil'ev YV, Lopez NI, Makarov A, Beckman JS, Voinov VG. Sequencing Grade Tandem Mass Spectrometry for Top-Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer. Anal Chem 2018; 90:10819-10827. [PMID: 30118589 DOI: 10.1021/acs.analchem.8b01901] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Compared to traditional collision induced dissociation methods, electron capture dissociation (ECD) provides more comprehensive characterization of large peptides and proteins as well as preserves labile post-translational modifications. However, ECD experiments are generally restricted to the high magnetic fields of FTICR-MS that enable the reaction of large polycations and electrons. Here, we demonstrate the use of an electromagnetostatic ECD cell to perform ECD and hybrid ECD methods utilizing 193 nm photons (ECuvPD) or collisional activation (EChcD) in a benchtop quadrupole-Orbitrap mass spectrometer. The electromagnetostatic ECD cell was designed to replace the transfer octapole between the quadrupole and C-trap. This implementation enabled facile installation of the ECD cell, and ions could be independently subjected to ECD, UVPD, HCD, or any combination. Initial benchmarking and characterization of fragmentation propensities for ECD, ECuvPD, and EChcD were performed using ubiquitin (8.6 kDa). ECD yielded extensive sequence coverage for low charge states of ubiquitin as well as for the larger protein carbonic anhydrase II (29 kDa), indicating pseudo-activated ion conditions. Additionally, relatively high numbers of d- and w-ions enable differentiation of isobaric isoleucine and leucine residues and suggest a distribution of electron energies yield hot-ECD type fragmentation. We report the most comprehensive characterization to date for model proteins up to 29 kDa and a monoclonal antibody at the subunit level. ECD, ECuvPD, and EChcD yielded 93, 95, and 91% sequence coverage, respectively, for carbonic anhydrase II (29 kDa), and targeted online analyses of monoclonal antibody subunits yielded 86% overall antibody sequence coverage.
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Affiliation(s)
- Jared B Shaw
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Bouelvard , Richland , Washington 99354 , United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , 3335 Innovation Bouelvard , Richland , Washington 99354 , United States
| | - Yury V Vasil'ev
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Nathan I Lopez
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen) GmbH , Hanna-Kunath Str. 11 , 28199 Bremen , Germany
| | - Joseph S Beckman
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Valery G Voinov
- e-MSion Inc. , 2121 NE Jack London Drive , Corvallis , Oregon 97330 , United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
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35
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Kechko O, Petrushanko I, Piatkov K, Mitkevich V, Makarov A. P1‐201: APOPTOSIS‐INDUCING EFFECT OF Aβ PEPTIDES IS ASSOCIATED WITH INHIBITION OF N‐END RULE PATHWAY PROTEOLYTIC ACTIVITY. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.206] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Olga Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, MoscowRussian Federation
| | - Irina Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, MoscowRussian Federation
| | - Konstantin Piatkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, MoscowRussian Federation
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, MoscowRussian Federation
| | - Alexander Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, MoscowRussian Federation
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36
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van de Waterbeemd M, Tamara S, Fort KL, Damoc E, Franc V, Bieri P, Itten M, Makarov A, Ban N, Heck AJR. Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nat Commun 2018; 9:2493. [PMID: 29950687 PMCID: PMC6021402 DOI: 10.1038/s41467-018-04853-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/28/2018] [Indexed: 11/08/2022] Open
Abstract
Biomolecular mass spectrometry has matured strongly over the past decades and has now reached a stage where it can provide deep insights into the structure and composition of large cellular assemblies. Here, we describe a three-tiered hybrid mass spectrometry approach that enables the dissection of macromolecular complexes in order to complement structural studies. To demonstrate the capabilities of the approach, we investigate ribosomes, large ribonucleoprotein particles consisting of a multitude of protein and RNA subunits. We identify sites of sequence processing, protein post-translational modifications, and the assembly and stoichiometry of individual ribosomal proteins in four distinct ribosomal particles of bacterial, plant and human origin. Amongst others, we report extensive cysteine methylation in the zinc finger domain of the human S27 protein, the heptameric stoichiometry of the chloroplastic stalk complex, the heterogeneous composition of human 40S ribosomal subunits and their association to the CrPV, and HCV internal ribosome entry site RNAs.
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Affiliation(s)
- Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands
- Netherlands Proteomics Center, 3584CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands
- Netherlands Proteomics Center, 3584CH, Utrecht, The Netherlands
| | - Kyle L Fort
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands
- Netherlands Proteomics Center, 3584CH, Utrecht, The Netherlands
- Thermo Fisher Scientific, 28199, Bremen, Germany
| | - Eugen Damoc
- Thermo Fisher Scientific, 28199, Bremen, Germany
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands
- Netherlands Proteomics Center, 3584CH, Utrecht, The Netherlands
| | - Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Martin Itten
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Alexander Makarov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands
- Thermo Fisher Scientific, 28199, Bremen, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584CH, The Netherlands.
- Netherlands Proteomics Center, 3584CH, Utrecht, The Netherlands.
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37
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Arutyunyan I, Fatkhudinov T, Elchaninov A, Makarov A, Vasyukova O, Usman N, Marey M, Volodina M, Kananykhina E, Lokhonina A, Bolshakova G, Goldshtein D, Sukhikh G. Understanding mechanisms of the umbilical cord-derived multipotent mesenchymal stromal cell-mediated recovery enhancement in rat model of limb ischemia. G&C 2018. [DOI: 10.23868/201805010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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38
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Sanders JD, Grinfeld D, Aizikov K, Makarov A, Holden DD, Brodbelt JS. Determination of Collision Cross-Sections of Protein Ions in an Orbitrap Mass Analyzer. Anal Chem 2018; 90:5896-5902. [DOI: 10.1021/acs.analchem.8b00724] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- James D. Sanders
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | | | | | | | - Dustin D. Holden
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
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39
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Voloshin S, Smoldovskaya O, Feyzkhanova G, Arefieva A, Pavlushkina L, Filatova T, Butvilovskaya V, Filippova M, Lysov Y, Shcherbo S, Makarov A, Rubina A, Zasedatelev A. Patterns of sensitization to inhalant and food allergens among pediatric patients from the Moscow region (Russian Federation). PLoS One 2018; 13:e0194775. [PMID: 29566093 PMCID: PMC5864043 DOI: 10.1371/journal.pone.0194775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 03/11/2018] [Indexed: 02/07/2023] Open
Abstract
The immunological profiles of human specific IgE (sIgE) and specific IgG4 (sIgG4) vary by genetic predisposition, living conditions in different geographical locations and patient’s age. The aim of our study was to analyze sIgE and sIgG4 patterns and their age-dependent changes in patients from the Moscow region. For identifying sIgE and sIgG4 profiles the blood samples from 513 patients aged 6 months to 17 years who were showing symptoms of allergic diseases were analyzed using microarrays containing 31 allergens. The highest sIgE prevalence was observed for birch pollen (32%) among pollen allergens, cat dander (24%) among indoor allergens, and egg whites (21%) among food allergens. The most common sIgG4 response was developed toward egg whites (80% of patients). Age-related elevation was identified for patients with increased sIgE to pollen allergens and indoor allergens (cat or dog dander and house dust mites). For each allergen, the proportion of cases with significant levels of sIgG4 appeared to increase with patients’ age. The data on allergen-specific sIgE and sIgG4 prevalence show both general trends and some local special aspects that are indicative for the Moscow region. This information should be useful in terms of epidemiology of allergic diseases.
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Affiliation(s)
- Sergei Voloshin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Smoldovskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Guzel Feyzkhanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alla Arefieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | - Marina Filippova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri Lysov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexander Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alla Rubina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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40
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Schmidt EM, Pudenzi MA, Santos JM, Angolini CFF, Pereira RCL, Rocha YS, Denisov E, Damoc E, Makarov A, Eberlin MN. Petroleomics via Orbitrap mass spectrometry with resolving power above 1 000 000 at m/z 200. RSC Adv 2018; 8:6183-6191. [PMID: 35539593 PMCID: PMC9078259 DOI: 10.1039/c7ra12509g] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/27/2018] [Indexed: 12/18/2022] Open
Abstract
The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches. Pertinent parameters that underpin the main figures of merit, that is, signal to noise ratios, dynamic range, spectral error, scan speed, mass accuracy and mass resolving power = Rp, and provide subsidies to develop these analyzers were tested. Comparisons are made with data obtained using the most common petroleomics instrument, which is a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), that has been used in the last decade in our laboratory for crude oil analysis providing Rp of 340 000 at m/z 400 with transients of 3 s duration, and has been extensively demonstrated to fulfill all major requirements for precise petroleomics investigations. The high-field compact MegaOrbitrap mass analyzer, when operated at an Rp = 840 000 at m/z 400 (Rp > 1 000 000 at m/z 200) with a detection time of 3 s, was found to be well suited for adequate characterization of crude oil. Accurate class classification and mass accuracy below 1 ppm was obtained leading to proper, comprehensive petroleomics characterization. The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization via classical petroleomics approaches.![]()
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Affiliation(s)
- Eduardo M. Schmidt
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Marcos A. Pudenzi
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Jandyson M. Santos
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | - Celio F. F. Angolini
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
| | | | | | | | | | | | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory
- Institute of Chemistry
- University of Campinas
- UNICAMP
- Campinas
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41
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Passarelli MK, Pirkl A, Moellers R, Grinfeld D, Kollmer F, Havelund R, Newman CF, Marshall PS, Arlinghaus H, Alexander MR, West A, Horning S, Niehuis E, Makarov A, Dollery CT, Gilmore IS. The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power. Nat Methods 2017; 14:1175-1183. [DOI: 10.1038/nmeth.4504] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
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42
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Reid DJ, Keener JE, Wheeler AP, Zambrano DE, Diesing JM, Reinhardt-Szyba M, Makarov A, Marty MT. Engineering Nanodisc Scaffold Proteins for Native Mass Spectrometry. Anal Chem 2017; 89:11189-11192. [PMID: 29048874 DOI: 10.1021/acs.analchem.7b03569] [Citation(s) in RCA: 34] [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: 12/13/2022]
Abstract
Lipoprotein nanodiscs are ideally suited for native mass spectrometry because they provide a relatively monodisperse nanoscale lipid bilayer environment for delivering membrane proteins into the gas phase. However, native mass spectrometry of nanodiscs produces complex spectra that can be challenging to assign unambiguously. To simplify interpretation of nanodisc spectra, we engineered a series of mutant membrane scaffold proteins (MSP) that do not affect nanodisc formation but shift the masses of nanodiscs in a controllable way, eliminating isobaric interference from the lipids. Moreover, by mixing two different belts before assembly, the stoichiometry of MSP is encoded in the peak shape, which allows the stoichiometry to be assigned unambiguously from a single spectrum. Finally, we demonstrate the use of mixed belt nanodiscs with embedded membrane proteins to confirm the dissociation of MSP prior to desolvation.
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Affiliation(s)
- Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Andrew P Wheeler
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Dane Evan Zambrano
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Jessica M Diesing
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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43
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Burdakov A, Azhannikov A, Astrelin V, Beklemishev A, Burmasov V, Derevyankin G, Ivanenko V, Ivanov I, Ivantsivsky M, Kandaurov I, Konyukhov V, Kotelnikov I, Kovenya V, Kozlinskaya T, Kuklin K, Kuznetsov A, Kuznetsov S, Lotov K, Timofeev I, Makarov A, Mekler K, Nikolaev V, Popov S, Postupaev V, Polosatkin S, Rovenskikh A, Shoshin A, Shvab I, Sinitsky S, Sulyaev Y, Stepanov V, Trunyov Y, Vyacheslavov L, Zhukov V, Zubairov E. Plasma Heating and Confinement in GOL-3 Multi Mirror Trap. Fusion Science and Technology 2017. [DOI: 10.13182/fst07-a1327] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- A. Burdakov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - A. Azhannikov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Astrelin
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - A. Beklemishev
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Burmasov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - G. Derevyankin
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Ivanenko
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - I. Ivanov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - M. Ivantsivsky
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - I. Kandaurov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Konyukhov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - I. Kotelnikov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Kovenya
- Institute of Computational Technologies, 630090, Novosibirsk Russia
| | - T. Kozlinskaya
- Institute of Computational Technologies, 630090, Novosibirsk Russia
| | - K. Kuklin
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - A. Kuznetsov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - S. Kuznetsov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - K. Lotov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - I. Timofeev
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - A. Makarov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - K. Mekler
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Nikolaev
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - S. Popov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Postupaev
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - S. Polosatkin
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - A. Rovenskikh
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - A. Shoshin
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - I. Shvab
- Institute of Computational Technologies, 630090, Novosibirsk Russia
| | - S. Sinitsky
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - Yu. Sulyaev
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Stepanov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - Yu. Trunyov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - L. Vyacheslavov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
| | - V. Zhukov
- Institute of Computational Technologies, 630090, Novosibirsk Russia
| | - Ed. Zubairov
- Budker Institute of Nuclear Physics, 630090, Novosibirsk, Russia
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44
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Burdakov A, Arzhannikov A, Astrelin V, Batkin V, Burmasov V, Derevyankin G, Ivanenko V, Ivanov I, Ivantsivskiy M, Kandaurov I, Konyukhov V, Kuklin K, Kuznetsov S, Makarov A, Makarov M, Mekler K, Polosatkin S, Popov S, Postupaev V, Rovenskikh A, Shoshin A, Sinitsky S, Stepanov V, Sulyaev Y, Trunev Y, Vyacheslavov L. Status and Prospects of GOL-3 Multiple-Mirror Trap. Fusion Science and Technology 2017. [DOI: 10.13182/fst09-a6984] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- A. Burdakov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State Technical University, 20 Karl Marx Avenue, Novosibirsk 630092, Russia
| | - A. Arzhannikov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - V. Astrelin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - V. Batkin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - V. Burmasov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - G. Derevyankin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - V. Ivanenko
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - I. Ivanov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - M. Ivantsivskiy
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State Technical University, 20 Karl Marx Avenue, Novosibirsk 630092, Russia
| | - I. Kandaurov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - V. Konyukhov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - K. Kuklin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - S. Kuznetsov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - A. Makarov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - M. Makarov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - K. Mekler
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - S. Polosatkin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - S. Popov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - V. Postupaev
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State Technical University, 20 Karl Marx Avenue, Novosibirsk 630092, Russia
| | - A. Rovenskikh
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - A. Shoshin
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - S. Sinitsky
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State Technical University, 20 Karl Marx Avenue, Novosibirsk 630092, Russia
| | - V. Stepanov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - Yu. Sulyaev
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - Yu. Trunev
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
| | - L. Vyacheslavov
- Budker Institute of Nuclear Physics, 11 Lavrentjev Avenue, Novosibirsk 630090, Russia
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Gao H, Makarov A, Smith RD. 2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives. J Am Soc Mass Spectrom 2017; 28:1248-1249. [PMID: 28417304 DOI: 10.1007/s13361-017-1664-5] [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]
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Arutyunyan I, Tenchurin T, Kananykhina E, Chernikov V, Vasyukova O, Elchaninov A, Makarov A, Korshunov A, Burov A, Podurovskaya Y, Chuprynin V, Uvarova E, Degtyarev D, Shepelev A, Mamagulashvili V, Kamyshinskiy R, Krasheninnikov S, Chvalun S, Fatkhudinov T. Nonwoven polycaprolactone scaffolds for tissue engineering: the choice of the structure and the method of cell seeding. Genes & Cells 2017. [DOI: 10.23868/201703009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Grinfeld D, Kopaev I, Skoblin M, Monastyrskiy M, Makarov A, Alimpiev S. Some aspects of space-charge effect calculation in high-resolution mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1047:59-63. [DOI: 10.1016/j.jchromb.2016.09.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/23/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
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Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO. Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer. J Proteomics 2017; 159:67-76. [PMID: 28242452 DOI: 10.1016/j.jprot.2017.02.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 10/25/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/27/2022]
Abstract
The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (~150kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal sample preparation. In a previous work we showed the potential of Orbitrap Fourier transform mass spectrometry (FTMS) combined with electron transfer dissociation (ETD) for the top-down investigation of an intact IgG1, resulting in ~30% sequence coverage. Here, we describe a top-down analysis of two IgGs1 (adalimumab and trastuzumab) and one IgG2 (panitumumab) performed with ETD on a mass spectrometer equipped with a high-field Orbitrap mass analyzer. For the IgGs1, sequence coverage comparable to the previous results was achieved in a two-fold reduced number of summed transients, which corresponds, taken together with the significantly increased spectra acquisition rate, to ~six-fold improvement in analysis time. Furthermore, we studied the influence of ion-ion interaction times on ETD product ions for IgGs1, and the differences in fragmentation behavior between IgGs1 and IgG2, which present structural differences. Overall, these results reinforce the hypothesis that gas phase dissociation using both energy threshold-based and radical-driven ion activations is directed to specific regions of the polypeptide chains mostly by the location of disulfide bonds. SIGNIFICANCE OF THE STUDY Compared with our previous report, the results presented herein demonstrate the power of technological advances of the next generation Orbitrap™ platform, including the use of a high-field compact (i.e., D20) Orbitrap mass analyzer, and a dedicated manipulation strategy for large protein ions (via their trapping in the HCD collision cell along with reduction of the pressure in the cell). Notably, these important developments became recently commercially available in the top-end Orbitrap platforms under the name of "Protein Mode". Furthermore, we continued exploring the advantages offered by the summation (averaging) of transients (time-domain data) for improving the signal-to-noise ratio of top-down mass spectra. Finally, for the first time we report the application of the hybrid ion activation technique that combines electron transfer dissociation and higher energy collisional dissociation, known as EThcD, on intact monoclonal antibodies. Under these specific instrumental parameters, EThcD produces a partially complementary fragmentation pattern compared to ETD, increasing the overall sequence coverage especially at the protein termini.
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Affiliation(s)
- Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Ayoub
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 46202 Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Eugen Damoc
- Thermo Fisher Scientific GmbH, 28199 Bremen, Germany
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California in San Diego, 92093 San Diego, CA, USA
| | | | - Alain Beck
- Centre d'Immunologie Pierre Fabre, 74160 St Julien-en-Genevois, France
| | - Yury O Tsybin
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Spectroswiss Sàrl, EPFL Innovation Park, 1015 Lausanne, Switzerland.
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Grinfeld D, Aizikov K, Kreutzmann A, Damoc E, Makarov A. Phase-Constrained Spectrum Deconvolution for Fourier Transform Mass Spectrometry. Anal Chem 2016; 89:1202-1211. [DOI: 10.1021/acs.analchem.6b03636] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmitry Grinfeld
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Konstantin Aizikov
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Arne Kreutzmann
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Eugen Damoc
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
| | - Alexander Makarov
- Thermo Fisher Scientific (Bremen), Hanna-Kunath Strasse 11, 28199 Bremen, Germany
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Abstract
Ephedrine and pseudoephedrine are stimulant drugs whose use is prohibited in athletic competition by the World Anti-Doping Agency (WADA) at very different threshold doping violation concentrations. We use a recently developed universal approach that integrates UV photofragmentation spectroscopy of cold ions with Orbitrap mass spectrometry (MS) for highly selective and highly sensitive identification of these diastereomers. Both species can be selectively detected at a solution concentration of a few tens of ng/mL, which is almost 3 orders of magnitude lower than the threshold concentration required by WADA. Relative concentrations of the isomers in solutions have been determined with the standard deviation of 3.1%, when the ions were cooled in an ion trap maintained at T = 6 K. Considering practical implementation of the method, we evaluated its performance for a simplified instrumentation. At an affordable elevated temperature of ∼70 K and with a low-maintenance midbandwidth optical parametric oscillator, a few second measurement should yield nearly the same selectivity and only ten times lower sensitivity than with the current research grade instrument.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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