1
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Wootton CA, Maillard J, Theisen A, Brabeck GF, Schat CL, Rüger CP, Afonso C, Giusti P. A Gated TIMS FTICR MS Instrument to Decipher Isomeric Content of Complex Organic Mixtures. Anal Chem 2024; 96:11343-11352. [PMID: 38973712 DOI: 10.1021/acs.analchem.4c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Modern research faces increasingly complex materials with a constant need for new analytical strategies that can provide deeper levels of chemical insight. Ultrahigh resolution mass spectrometry (MS), particularly Fourier transform ion cyclotron resonance (FTICR) MS, has provided a robust analytical foundation. However, MS alone offers limited structural information. Here, we present the first implementation and results from an FTICR MS with fully integrated dual accumulation analysis with gated trapped ion mobility spectrometry (gTIMS) capability. The drastically extended charge capacity and parallel accumulation facilitate the analysis of complex mixtures. We achieved a high dynamic range of 4 orders of magnitude within a single FTICR acquisition event. Simultaneously, the valuable linear relationship between the TIMS elution voltage and reduced mobility was retained over a wide mobility range. Benchmarking the instrument performance with Suwannee River fulvic acid (SRFA) by variable ramp gTIMS analysis allowed separation and unambiguous assignment of different charge state distributions. Application to bio-oils has proven the capability to distinguish the isomeric diversity in these ultracomplex samples, while maintaining the expected FTICR MS resolving power and mass accuracy. Valuable information about the molecular distribution, isomeric diversity, and main molecular differences could directly be extracted within the analysis time of a classical "dilute and shoot" direct infusion experiment. The development of this fully integrated and flexible gTIMS with FTICR MS analysis possesses the potential to significantly change the current landscape of high-resolution mass spectrometric analysis of complex mixtures through the added insight of isomeric complexity afforded by TIMS. The exploration of the added IMS dimension promises transformative effects across diverse fields including energy transition, environmental studies, and biological research.
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Affiliation(s)
| | - Julien Maillard
- TotalEnergies One Tech, R&D, Downstream Processes & Polymers, TotalEnergies Research & Technology Gonfreville, BP 27, 76700 Harfleur, France
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Alina Theisen
- Bruker Daltonics GmbH & Co. Kg, 28359 Bremen, Germany
| | | | | | - Christopher P Rüger
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
| | - Carlos Afonso
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, 76000 Rouen, France
| | - Pierre Giusti
- TotalEnergies One Tech, R&D, Downstream Processes & Polymers, TotalEnergies Research & Technology Gonfreville, BP 27, 76700 Harfleur, France
- International Joint Laboratory, iC2MC: Complex Matrices Molecular Characterization, TRTG, BP 27, 76700 Harfleur, France
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, 76000 Rouen, France
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2
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Perchepied S, Zhou Z, Mitulović G, Eeltink S. Exploiting ion-mobility mass spectrometry for unraveling proteome complexity. J Sep Sci 2023; 46:e2300512. [PMID: 37746674 DOI: 10.1002/jssc.202300512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) is experiencing rapid growth in proteomic studies, driven by its enhancements in dynamic range and throughput, increasing the quantitation precision, and the depth of proteome coverage. The core principle of ion mobility spectrometry is to separate ions in an inert gas under the influence of an electric field based on differences in drift time. This minireview provides an introduction to IMS operation modes and a description of advantages and limitations is presented. Moreover, the principles of trapped IMS-MS (TIMS-MS), including parallel accumulation-serial fragmentation are discussed. Finally, emerging applications linked to TIMS focusing on sample throughput (in clinical proteomics) and sensitivity (single-cell proteomics) are reviewed, and the possibilities of intact protein analysis are discussed.
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Affiliation(s)
- Stan Perchepied
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Zhuoheng Zhou
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Sebastiaan Eeltink
- Department of Chemical Engineering, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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3
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Leyva D, Usman Tariq M, Jaffé R, Saeed F, Fernandez-Lima F. Description of Dissolved Organic Matter Transformational Networks at the Molecular Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2672-2681. [PMID: 36724500 DOI: 10.1021/acs.est.2c04715] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Dissolved Organic Matter (DOM) is an important component of the global carbon cycle. Unscrambling the structural footprint of DOM is key to understand its biogeochemical transformations at the mechanistic level. Although numerous studies have improved our knowledge of DOM chemical makeup, its three-dimensional picture remains largely unrevealed. In this work, we compare four solid phase extracted (SPE) DOM samples from three different freshwater ecosystems using high resolution mobility and ultrahigh-resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FT-ICR MS/MS). Structural families were identified based on neutral losses at the level of nominal mass using continuous accumulation of selected ions-collision induced dissociation (CASI-CID)FT-ICR MS/MS. Comparison of the structural families indicated dissimilarities in the structural footprint of this sample set. The structural family representation using Cytoscape software revealed characteristic clustering patterns among the DOM samples, thus confirming clear differences at the structural level (Only 10% is common across the four samples.). The analysis at the level of neutral loss-based functionalities suggests that hydration and carboxylation are ubiquitous transformational processes across the three ecosystems. In contrast, transformation mechanisms involving methoxy moieties may be constrained in estuarine systems due to extensive upstream lignin biodegradation. The inclusion of the isomeric content (mobility measurements at the level of chemical formula) in the structural family description suggests that additional transformation pathways and/or source variations are possible and account for the dissimilarities observed. While the structural character of more and diverse types of DOM samples needs to be assessed and added to this database, the results presented here demonstrate that Graph-DOM is a powerful tool capable of providing novel information on the DOM chemical footprint, based on structural interconnections of precursor molecules generated by fragmentation pathways and collisional cross sections.
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Affiliation(s)
- Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida33199, United States
| | - Muhammad Usman Tariq
- School of Computing and Information Science, Florida International University, Miami, Florida33199, United States
| | - Rudolf Jaffé
- Institute of Environment and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida33199, United States
| | - Fahad Saeed
- School of Computing and Information Science, Florida International University, Miami, Florida33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida33199, United States
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4
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Atakay M. Monitoring Conformational Changes of Lysozyme–Polyelectrolyte Complexes Using Trapped Ion Mobility-Mass Spectrometry (IM-MS). ANAL LETT 2023. [DOI: 10.1080/00032719.2023.2173768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Mehmet Atakay
- Department of Chemistry, Hacettepe University, Ankara, Turkey
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5
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Seeing the complete picture: proteins in top-down mass spectrometry. Essays Biochem 2022; 67:283-300. [PMID: 36468679 DOI: 10.1042/ebc20220098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Abstract
Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.
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Chang D, Zaia J. Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data. MASS SPECTROMETRY REVIEWS 2022; 41:922-937. [PMID: 33764573 DOI: 10.1002/mas.21692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/24/2020] [Accepted: 03/11/2021] [Indexed: 05/18/2023]
Abstract
Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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A Comprehensive Study of Gradient Conditions for Deep Proteome Discovery in a Complex Protein Matrix. Int J Mol Sci 2022; 23:ijms231911714. [PMID: 36233016 PMCID: PMC9569591 DOI: 10.3390/ijms231911714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/28/2022] Open
Abstract
Bottom–up mass-spectrometry-based proteomics is a well-developed technology based on complex peptide mixtures from proteolytic cleavage of proteins and is widely applied in protein identification, characterization, and quantitation. A tims-ToF mass spectrometer is an excellent platform for bottom–up proteomics studies due to its rapid acquisition with high sensitivity. It remains challenging for bottom–up proteomics approaches to achieve 100% proteome coverage. Liquid chromatography (LC) is commonly used prior to mass spectrometry (MS) analysis to fractionate peptide mixtures, and the LC gradient can affect the peptide fractionation and proteome coverage. We investigated the effects of gradient type and time duration to find optimal gradient conditions. Five gradient types (linear, logarithm-like, exponent-like, stepwise, and step-linear), three different gradient lengths (22 min, 44 min, and 66 min), two sample loading amounts (100 ng and 200 ng), and two loading conditions (the use of trap column and no trap column) were studied. The effect of these chromatography variables on protein groups, peptides, and spectral counts using HeLa cell digests was explored. The results indicate that (1) a step-linear gradient performs best among the five gradient types studied; (2) the optimal gradient duration depends on protein sample loading amount; (3) the use of a trap column helps to enhance protein identification, especially low-abundance proteins; (4) MSFragger and PEAKS Studio have high similarity in protein group identification; (5) MSFragger identified more protein groups among the different gradient conditions compared to PEAKS Studio; and (6) combining results from both database search engines can expand identified protein groups by 9–11%.
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Delvaux A, Rathahao-Paris E, Alves S. Different ion mobility-mass spectrometry coupling techniques to promote metabolomics. MASS SPECTROMETRY REVIEWS 2022; 41:695-721. [PMID: 33492707 DOI: 10.1002/mas.21685] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Metabolomics has become increasingly popular in recent years for many applications ranging from clinical diagnosis, human health to biotechnological questioning. Despite technological advances, metabolomic studies are still currently limited by the difficulty of identifying all metabolites, a class of compounds with great chemical diversity. Although lengthy chromatographic analyses are often used to obtain comprehensive data, many isobar and isomer metabolites still remain unresolved, which is a critical point for the compound identification. Currently, ion mobility spectrometry is being explored in metabolomics as a way to improve metabolome coverage, analysis throughput and isomer separation. In this review, all the steps of a typical workflow for untargeted metabolomics are discussed considering the use of an ion mobility instrument. An overview of metabolomics is first presented followed by a brief description of ion mobility instrumentation. The ion mobility potential for complex mixture analysis is discussed regarding its coupling with a mass spectrometer alone, providing gas-phase separation before mass analysis as well as its combination with different separation platforms (conventional hyphenation but also multidimensional ion mobility couplings), offering multidimensional separation. Various instrumental and analytical conditions for improving the ion mobility separation are also described. Finally, data mining, including software packages and visualization approaches, as well as the construction of ion mobility databases for the metabolite identification are examined.
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Affiliation(s)
- Aurélie Delvaux
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
| | - Estelle Rathahao-Paris
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, 91191, France
| | - Sandra Alves
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, 75005, France
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9
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Ion Mobility Mass Spectrometry for Structural Elucidation of Petroleum Compounds. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Korzhenko O, Führer P, Göldner V, Olthuis W, Odijk M, Karst U. Microfluidic Electrochemistry Meets Trapped Ion Mobility Spectrometry and High-Resolution Mass Spectrometry-In Situ Generation, Separation, and Detection of Isomeric Conjugates of Paracetamol and Ethoxyquin. Anal Chem 2021; 93:12740-12747. [PMID: 34495637 DOI: 10.1021/acs.analchem.1c02791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the last 3 decades, electrochemistry (EC) has been successfully applied in phase I and phase II metabolism simulation studies. The electrochemically generated phase I metabolite-like oxidation products can react with selected reagents to form phase II conjugates. During conjugate formation, the generation of isomeric compounds is possible. Such isomeric conjugates are often separated by high-performance liquid chromatography (HPLC). Here, we demonstrate a powerful approach that combines EC with ion mobility spectrometry to separate possible isomeric conjugates. In detail, we present the hyphenation of a microfluidic electrochemical chip with an integrated mixer coupled online to trapped ion mobility spectrometry (TIMS) and time-of-flight high-resolution mass spectrometry (ToF-HRMS), briefly chipEC-TIMS-ToF-HRMS. This novel method achieves results in several minutes, which is much faster than traditional separation approaches like HPLC, and was applied to the drug paracetamol and the controversial feed preservative ethoxyquin. The analytes were oxidized in situ in the electrochemical microfluidic chip under formation of reactive intermediates and mixed with different thiol-containing reagents to form conjugates. These were analyzed by TIMS-ToF-HRMS to identify possible isomers. It was observed that the oxidation products of both paracetamol and ethoxyquin form two isomeric conjugates, which are characterized by different ion mobilities, with each reagent. Therefore, using this hyphenated technique, it is possible to not only form reactive oxidation products and their conjugates in situ but also separate and detect these isomeric conjugates within only a few minutes.
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Affiliation(s)
- Oxana Korzhenko
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Pascal Führer
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Valentin Göldner
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany.,International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstr. 40, 48149 Münster, Germany
| | - Wouter Olthuis
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Mathieu Odijk
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany.,International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstr. 40, 48149 Münster, Germany
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11
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Larson EJ, Roberts DS, Melby JA, Buck KM, Zhu Y, Zhou S, Han L, Zhang Q, Ge Y. High-Throughput Multi-attribute Analysis of Antibody-Drug Conjugates Enabled by Trapped Ion Mobility Spectrometry and Top-Down Mass Spectrometry. Anal Chem 2021; 93:10013-10021. [PMID: 34258999 PMCID: PMC8319120 DOI: 10.1021/acs.analchem.1c00150] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibody-drug conjugates (ADCs) are one of the fastest growing classes of anticancer therapies. Combining the high targeting specificity of monoclonal antibodies (mAbs) with cytotoxic small molecule drugs, ADCs are complex molecular entities that are intrinsically heterogeneous. Primary sequence variants, varied drug-to-antibody ratio (DAR) species, and conformational changes in the starting mAb structure upon drug conjugation must be monitored to ensure the safety and efficacy of ADCs. Herein, we have developed a high-throughput method for the analysis of cysteine-linked ADCs using trapped ion mobility spectrometry (TIMS) combined with top-down mass spectrometry (MS) on a Bruker timsTOF Pro. This method can analyze ADCs (∼150 kDa) by TIMS followed by a three-tiered top-down MS characterization strategy for multi-attribute analysis. First, the charge state distribution and DAR value of the ADC are monitored (MS1). Second, the intact mass of subunits dissociated from the ADC by low-energy collision-induced dissociation (CID) is determined (MS2). Third, the primary sequence for the dissociated subunits is characterized by CID fragmentation using elevated collisional energies (MS3). We further automate this workflow by directly injecting the ADC and using MS segmentation to obtain all three tiers of MS information in a single 3-min run. Overall, this work highlights a multi-attribute top-down MS characterization method that possesses unparalleled speed for high-throughput characterization of ADCs.
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Affiliation(s)
- Eli J Larson
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
| | - Shiyue Zhou
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, United States
| | - Linjie Han
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, United States
| | - Qunying Zhang
- Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, Illinois 60064, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin - Madison, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin, 1111 Highland Avenue., Madison, Wisconsin 53705, United States
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12
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Law KP, He W, Tao J, Zhang C. Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:658781. [PMID: 34276593 PMCID: PMC8281238 DOI: 10.3389/fmicb.2021.658781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5′-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.
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Affiliation(s)
- Kai P Law
- SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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13
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Olanrewaju CA, Ramirez CE, Fernandez-Lima F. Comprehensive Screening of Polycyclic Aromatic Hydrocarbons and Similar Compounds Using GC-APLI-TIMS-TOFMS/GC-EI-MS. Anal Chem 2021; 93:6080-6087. [PMID: 33835784 DOI: 10.1021/acs.analchem.0c04525] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present work, a novel workflow based on complementary gas-phase separations for the identification of isomeric PAHs from complex mixtures is described. This is the first report on the coupling of gas chromatography (GC), atmospheric pressure laser ionization (APLI), and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) for the characterization of polycyclic aromatic hydrocarbons. Over a hundred known unknowns are uniquely identified based on the molecular ion retention indices I (5%), mobility (RSD < 0.6% and R = 50-90 with Sr = 0.18 V/ms), mobility-based theoretical candidate assignment (<3%), accurate mass chemical formula assignment (<2 ppm), and electron impact fragmentation pattern and database search. The advantages of theoretical modeling of PAHs and similar compounds were evaluated using candidate structures ranked by retention indices and fragmentation pattern from GC-EI-MS data sets. Over 20 PAH isomeric and deuterated standards were utilized for the GC-APLI-TIMS-TOF MS workflow validation. Noteworthy is the analytical capability for untargeted screening of isomeric and isobaric compounds with additional characterization metrics not available in traditional GC-EI-MSn workflows.
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Affiliation(s)
- Clement A Olanrewaju
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Cesar E Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Advanced Mass Spectrometry Facility, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Advanced Mass Spectrometry Facility, Florida International University, Miami, Florida 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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14
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He D, Wang K, Pang Y, He C, Li P, Li Y, Xiao S, Shi Q, Sun Y. Hydrological management constraints on the chemistry of dissolved organic matter in the Three Gorges Reservoir. WATER RESEARCH 2020; 187:116413. [PMID: 32980606 DOI: 10.1016/j.watres.2020.116413] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Reservoirs are well known as a far-reaching human modification on the functions of natural river networks. However, changes in the chemistry and reactivity of dissolved organic matter (DOM) responding to hydrological management for water retention structures, and its influence on the river carbon cycle, remain poorly understood. Here we show that hydrological management does shape the molecular composition of DOM in the world's largest Three Gorges Reservoir, as revealed by optical spectroscopy and ultrahigh-resolution mass spectrometry. Relatively higher terrestrial input, molecular complexity, isomeric complexity, and environmental stability of DOM were observed during the storage period, whereas the inverse occurred during the drainage period. The results demonstrate that the hydrodynamic processes, which are mainly controlled by water intrusion from mainstream to tributaries, are likely the underlying mechanism controlling DOM chemistry. Integrated with observations from worldwide river reservoirs, the DOM degradation experiments suggest that reservoir hydrological management would enhance DOM mineralization, thereby increase CO2 emission and change the river carbon cycle.
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Affiliation(s)
- Ding He
- Organic Geochemistry Unit, School of Earth Sciences, Zhejiang University, Hangzhou 310027, China
| | - Kai Wang
- Organic Geochemistry Unit, School of Earth Sciences, Zhejiang University, Hangzhou 310027, China
| | - Yu Pang
- Organic Geochemistry Unit, School of Earth Sciences, Zhejiang University, Hangzhou 310027, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Changping District, Beijing 102249, China
| | - Penghui Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Yunyun Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Changping District, Beijing 102249, China
| | - Shangbin Xiao
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang 443002, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Changping District, Beijing 102249, China
| | - Yongge Sun
- Organic Geochemistry Unit, School of Earth Sciences, Zhejiang University, Hangzhou 310027, China.
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15
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Leyva D, Jaffe R, Fernandez-Lima F. Structural Characterization of Dissolved Organic Matter at the Chemical Formula Level Using TIMS-FT-ICR MS/MS. Anal Chem 2020; 92:11960-11966. [PMID: 32786462 DOI: 10.1021/acs.analchem.0c02347] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
TIMS-FT-ICR MS is an important alternative to study the isomeric diversity and elemental composition of complex mixtures. While the chemical structure of many compounds in the dissolved organic matter (DOM) remains largely unknown, the high structural diversity has been described at the molecular level using chemical formulas. In this study, we further push the boundaries of TIMS-FT-ICR MS by performing chemical formula-based ion mobility and tandem MS analysis for the structural characterization of DOM. The workflow described is capable to mobility select (R ∼ 100) and isolate molecular ion signals (Δm/z = 0.036) in the ICR cell, using single-shot ejections after broadband ejections and MS/MS based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The workflow results are compared to alternative TIMS-q-FT-ICR MS/MS experiments with quadrupole isolation at nominal mass (∼1 Da). The technology is demonstrated with isomeric and isobaric mixtures (e.g., 4-methoxy-1-naphthoic acid, 2-methoxy-1-naphthoic acid, decanedioic acid) and applied to the characterization of DOM. The application of this new methodology to the analysis of a DOM is illustrated by the isolation of the molecular ion [C18H18O10-H]- in the presence of other isobars at nominal mass 393. Five IMS bands were assigned to the heterogeneous ion mobility profile of [C18H18O10-H]-, and candidate structures from the PubChem database were screened based on their ion mobility and the MS/MS matching score. This approach overcomes traditional challenges associated with the similarity of fragmentation patterns of DOM samples (e.g., common neutral losses of H2O, CO2, and CH2-H2O) by narrowing down the isomeric candidate structures using the mobility domain.
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16
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Palacio Lozano DC, Thomas MJ, Jones HE, Barrow MP. Petroleomics: Tools, Challenges, and Developments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:405-430. [PMID: 32197051 DOI: 10.1146/annurev-anchem-091619-091824] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detailed molecular characterization of petroleum-related samples by mass spectrometry, often referred to as petroleomics, continues to present significant analytical challenges. As a result, petroleomics continues to be a driving force for the development of new ultrahigh resolution instrumentation, experimental methods, and data analysis procedures. Recent advances in ionization, resolving power, mass accuracy, and the use of separation methods, have allowed for record levels of compositional detail to be obtained for petroleum-related samples. To address the growing size and complexity of the data generated, vital software tools for data processing, analysis, and visualization continue to be developed. The insights gained impact upon the fields of energy and environmental science and the petrochemical industry, among others. In addition to advancing the understanding of one of nature's most complex mixtures, advances in petroleomics methodologies are being adapted for the study of other sample types, resulting in direct benefits to other fields.
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Affiliation(s)
| | - Mary J Thomas
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom;
- Molecular Analytical Sciences Centre for Doctoral Training, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hugh E Jones
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom;
- Molecular Analytical Sciences Centre for Doctoral Training, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom;
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17
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Selliez L, Maillard J, Cherville B, Gautier T, Thirkell L, Gaubicher B, Schmitz-Afonso I, Afonso C, Briois C, Carrasco N. High-resolution mass spectrometry for future space missions: Comparative analysis of complex organic matter with LAb-CosmOrbitrap and laser desorption/ionization Fourier transform ion cyclotron resonance. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8645. [PMID: 31671213 DOI: 10.1002/rcm.8645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/26/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Mass spectrometers are regularly boarded on spacecraft for the exploration of the Solar System. A better understanding of the origin, distribution and evolution of organic matter and its relationships with inorganic matter in different extra-terrestrial environments requires the development of innovative space tools, described as Ultra-High-Resolution Mass Spectrometry (UHRMS) instruments. METHODS Analyses of a complex organic material simulating extraterrestrial matter (Titan's tholins) are performed with a homemade space-designed Orbitrap™ equipped with a laser ablation ionization source at 266 nm: the LAb-CosmOrbitrap. Mass spectra are obtained using only one laser shot and transient duration of 838 ms. A comparison is made on the same sample with a laboratory benchmark mass spectrometer: a Fourier Transform Ion Cyclotron Resonance equipped with a laser desorption ionization source at 355 nm (LDI-FTICR) allowing accumulation of 20,000 laser shots. RESULTS Mass spectra and attributions of molecular formulae based on the peaks detected by both techniques show significant similarities. Detection and identification of the same species are validated. The formation of clusters ions with the LAb-CosmOrbitrap is also presented. This specific feature brings informative and unusual indirect detections about the chemical compounds constituting Titan's tholins. In particular, the detection of HCN confirms previous results obtained with laboratory Electrospray Ionization (ESI)-UHRMS studies about the understanding of polymeric patterns for the formation of tholins. CONCLUSIONS The capabilities of the LAb-CosmOrbitrap to decipher complex organic mixtures using single laser shot and a short transient are highlighted. In agreement with results provided by a commercial FTICR instrument in the laboratory, we demonstrate in this work the relevance of a space laser-CosmOrbitrap instrument for future planetary exploration.
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Affiliation(s)
- Laura Selliez
- Laboratoire de physique et Chimie de l'Environnement et de l'Espace (LPC2E), Orléans, France
- Laboratoire Atmosphères, Milieux et Observations Spatiales (LATMOS), Guyancourt, France
| | - Julien Maillard
- Laboratoire Atmosphères, Milieux et Observations Spatiales (LATMOS), Guyancourt, France
- Université de Rouen, Laboratoire COBRA UMR 6014 & FR 3038, IRCOF, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Barnabe Cherville
- Laboratoire de physique et Chimie de l'Environnement et de l'Espace (LPC2E), Orléans, France
| | - Thomas Gautier
- Laboratoire Atmosphères, Milieux et Observations Spatiales (LATMOS), Guyancourt, France
| | - Laurent Thirkell
- Laboratoire de physique et Chimie de l'Environnement et de l'Espace (LPC2E), Orléans, France
| | - Bertrand Gaubicher
- Laboratoire de physique et Chimie de l'Environnement et de l'Espace (LPC2E), Orléans, France
| | - Isabelle Schmitz-Afonso
- Université de Rouen, Laboratoire COBRA UMR 6014 & FR 3038, IRCOF, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Carlos Afonso
- Université de Rouen, Laboratoire COBRA UMR 6014 & FR 3038, IRCOF, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Christelle Briois
- Laboratoire de physique et Chimie de l'Environnement et de l'Espace (LPC2E), Orléans, France
| | - Nathalie Carrasco
- Laboratoire Atmosphères, Milieux et Observations Spatiales (LATMOS), Guyancourt, France
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18
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Pan Q, Zhuo X, He C, Zhang Y, Shi Q. Validation and Evaluation of High-Resolution Orbitrap Mass Spectrometry on Molecular Characterization of Dissolved Organic Matter. ACS OMEGA 2020; 5:5372-5379. [PMID: 32201827 PMCID: PMC7081437 DOI: 10.1021/acsomega.9b04411] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/20/2020] [Indexed: 05/13/2023]
Abstract
Molecular composition of dissolved organic matter (DOM) is a hot topic in subjects such as environmental science and geochemistry. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been applied to molecular composition characterization of DOM successfully. However, high instrument and maintenance costs have constrained its wider application. A high-resolution Orbitrap mass spectrometer (Orbitrap MS) can provide approximately 500,000 resolving power (at m/z 200), which is potentially capable of characterizing the molecular composition of DOM. In this paper, the application of high-resolution Orbitrap MS was evaluated by comparing with FT-ICR MS in the aspect of resolution, mass distribution, detection dynamic range, and isotopic peak intensity ratio. The impact of instrument parameters of Orbitrap MS was further investigated, which includes ionization, ion transfer, and mass detection. The result shows that the high-resolution Orbitrap MS is capable or even preferable for molecular characterization of DOM. However, the peak intensity distributions are dependent on the instrument parameters, which could affect the environmental impact assessment caused by the sample itself. The result indicates that development of a universal and comparable method is of great demand.
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Affiliation(s)
- Qiong Pan
- State Key Laboratory of Heavy Oil Processing,
Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing,
Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing,
Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
| | - Yahe Zhang
- State Key Laboratory of Heavy Oil Processing,
Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing,
Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China
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19
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Fangmeyer J, Scheeren SG, Schmid R, Karst U. Fast Online Separation and Identification of Electrochemically Generated Isomeric Oxidation Products by Trapped Ion Mobility–Mass Spectrometry. Anal Chem 2019; 92:1205-1210. [DOI: 10.1021/acs.analchem.9b04337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Fangmeyer
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
| | - Simon G. Scheeren
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
| | - Robin Schmid
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
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20
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Ridgeway ME, Bleiholder C, Mann M, Park MA. Trends in trapped ion mobility – Mass spectrometry instrumentation. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.03.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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21
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Rüger CP, Maillard J, Le Maître J, Ridgeway M, Thompson CJ, Schmitz-Afonso I, Gautier T, Carrasco N, Park MA, Giusti P, Afonso C. Structural Study of Analogues of Titan's Haze by Trapped Ion Mobility Coupled with a Fourier Transform Ion Cyclotron Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1169-1173. [PMID: 31066005 DOI: 10.1007/s13361-019-02205-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
The aerosols present in the atmosphere of the Saturn's moon Titan are of particular planetary science interest and several spacecraft missions are already allowed to gather spectroscopic data. Titan haze's analogs, so-called tholins, were produced on earth to push forward the comprehension of their formation and properties. In this study, this highly complex mixture was analyzed here for the first time by trapped ion mobility spectrometry coupled to ultra-high resolution mass spectrometry (FTICR MS). Electrospray ionization revealed the characteristic CHNx-class components, with CHN5-6 and DBE 6-7 most abundant. Deploying specialized visualization, enabled by accurate mass measurements and elemental composition assignments, the adapted Kendrick mass defect analysis highlights the C2H3N homolog series, whereas the nitrogen-modified van Krevelen diagram exhibits a clear trend towards H/C 1.5 and N/C 0.5. More interestingly, the representation of m/z versus collision cross section (CCS) allowed hypothesizing a ramified N-PAH structural motif. State-of-the-art IMS is currently not able to resolve the isomeric continuum of ultra-complex mixtures; thus, peak parameters other than the CCS value are explored. As such, analyzing the mobility peak width versus m/z shows a linear increase in isomeric diversity between m/z 170 and 350 and a near plateau in diversity at higher m/z for the N-PAH-like structure. Due to the high complexity of the sample, these structural insights are only to be revealed by TIMS-FTICR MS.
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Affiliation(s)
- Christopher P Rüger
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France.
| | - Julien Maillard
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | - Johann Le Maître
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
- TOTAL Refining and Chemicals, Total Research and Technologies Gonfreville, 76700 Harfleur, France
| | | | | | - Isabelle Schmitz-Afonso
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
| | - Thomas Gautier
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | - Nathalie Carrasco
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | | | - Pierre Giusti
- TOTAL Refining and Chemicals, Total Research and Technologies Gonfreville, 76700 Harfleur, France
| | - Carlos Afonso
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
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22
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Gao Y, Wang W, He C, Fang Z, Zhang Y, Shi Q. Fractionation and molecular characterization of natural organic matter (NOM) by solid-phase extraction followed by FT-ICR MS and ion mobility MS. Anal Bioanal Chem 2019; 411:6343-6352. [DOI: 10.1007/s00216-019-01943-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/05/2019] [Accepted: 05/24/2019] [Indexed: 10/26/2022]
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23
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Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS OMEGA 2019; 4:3619-3626. [PMID: 30842985 PMCID: PMC6396120 DOI: 10.1021/acsomega.8b02887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/11/2019] [Indexed: 05/14/2023]
Abstract
Topoisomerases are important complex enzymes that modulate DNA topology to maintain chromosome superstructure and integrity. These enzymes are involved in many cellular processes that resolve specific DNA superstructures and intermediates. The low abundance combined with the biological heterogeneity of relevant intermediates of topoisomerases makes their structural information not readily accessible using traditional structural biology tools (e.g., NMR and X-ray crystallography). In the present work, a second-generation trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used to study Escherichia coli topoisomerase IA (EcTopIA) and variola virus topoisomerase IB (vTopIB) as well as their complexes with a single-stranded DNA and a stem-loop DNA under native conditions. The higher trapping efficiency and extended mass range of the new, convex TIMS geometry allowed for the separation and identification of multiple conformational states for the two topoisomerases and their DNA complexes. Inspection of the conformational space of EcTopIA and vTopIB in complex with DNA showed that upon DNA binding, the number of conformational states is significantly reduced, suggesting that the DNA binding selects for a narrow range of conformers restricted by the interaction with the DNA substrate. The large microheterogeneity observed for the two DNA binding proteins suggests that they can have multiple biological functions. This work highlights the potential of TIMS-MS for the structural investigations of intrinsically disordered proteins (e.g., DNA binding proteins) as a way to gain a better understanding of the mechanisms involved in DNA substrate recognition, binding, and assembly of the catalytically active enzyme-DNA complex.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
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24
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Leyva D, Tose LV, Porter J, Wolff J, Jaffé R, Fernandez-Lima F. Understanding the structural complexity of dissolved organic matter: isomeric diversity. Faraday Discuss 2019; 218:431-440. [DOI: 10.1039/c8fd00221e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, the advantages of ESI-TIMS-FT-ICR MS to address the isomeric content of dissolved organic matter are studied.
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Affiliation(s)
- Dennys Leyva
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
- Southeast Environmental Research Center
| | - Lilian V. Tose
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Jacob Porter
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | | | - Rudolf Jaffé
- Southeast Environmental Research Center
- Florida International University
- Miami
- USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
- Biomolecular Sciences Institute
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25
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Larriba-Andaluz C, Chen X, Nahin M, Wu T, Fukushima N. Analysis of Ion Motion and Diffusion Confinement in Inverted Drift Tubes and Trapped Ion Mobility Spectrometry Devices. Anal Chem 2018; 91:919-927. [DOI: 10.1021/acs.analchem.8b03930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Xi Chen
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
- Purdue University, West Lafayette, Indiana 47907, United States
| | - Minal Nahin
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Tianyang Wu
- Department of Mechanical Engineering, Indiana University−Purdue University Indianapolis (IUPUI), 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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