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Hupatz H, Rahu I, Wang WC, Peets P, Palm EH, Kruve A. Critical review on in silico methods for structural annotation of chemicals detected with LC/HRMS non-targeted screening. Anal Bioanal Chem 2024:10.1007/s00216-024-05471-x. [PMID: 39138659 DOI: 10.1007/s00216-024-05471-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024]
Abstract
Non-targeted screening with liquid chromatography coupled to high-resolution mass spectrometry (LC/HRMS) is increasingly leveraging in silico methods, including machine learning, to obtain candidate structures for structural annotation of LC/HRMS features and their further prioritization. Candidate structures are commonly retrieved based on the tandem mass spectral information either from spectral or structural databases; however, the vast majority of the detected LC/HRMS features remain unannotated, constituting what we refer to as a part of the unknown chemical space. Recently, the exploration of this chemical space has become accessible through generative models. Furthermore, the evaluation of the candidate structures benefits from the complementary empirical analytical information such as retention time, collision cross section values, and ionization type. In this critical review, we provide an overview of the current approaches for retrieving and prioritizing candidate structures. These approaches come with their own set of advantages and limitations, as we showcase in the example of structural annotation of ten known and ten unknown LC/HRMS features. We emphasize that these limitations stem from both experimental and computational considerations. Finally, we highlight three key considerations for the future development of in silico methods.
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Affiliation(s)
- Henrik Hupatz
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden
- Stockholm University Center for Circular and Sustainable Systems (SUCCeSS), Stockholm University, 106 91, Stockholm, Sweden
| | - Ida Rahu
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden.
| | - Wei-Chieh Wang
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden
| | - Pilleriin Peets
- Institute of Biodiversity, Faculty of Biological Science, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Emma H Palm
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367, Belvaux, Luxembourg
| | - Anneli Kruve
- Department of Materials and Environmental Chemistry, Stockholm University, Svante Arrhenius Väg 16, 114 18, Stockholm, Sweden.
- Stockholm University Center for Circular and Sustainable Systems (SUCCeSS), Stockholm University, 106 91, Stockholm, Sweden.
- Department of Environmental Science, Stockholm University, Svante Arrhenius Väg 8, 114 18, Stockholm, Sweden.
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2
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Schaefer C, Lippmann M, Schindler C, Beukers M, Beijer N, Hitzemann M, van de Kamp B, Peters R, Knotter J, Zimmermann S. Pursuing drug laboratories: Analysis of drug precursors with High Kinetic Energy Ion Mobility Spectrometry. Forensic Sci Int 2024; 363:112196. [PMID: 39151243 DOI: 10.1016/j.forsciint.2024.112196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS) is a technique for rapid and reliable detection of trace compounds down to ppbV-levels within one second. Compared to classical IMS operating at ambient pressure and providing the ion mobility at low electric fields, HiKE-IMS can also provide the analyte-specific field dependence of the ion mobility and a fragmentation pattern at high reduced electric field strengths. The additional information about the analyte obtained by varying the reduced electric field strength can contribute to reliable detection. Furthermore, the reduced number of ion-molecule reactions at the low operating pressure of 10 - 40 mbar and the shorter reaction times reduce the impact of competing ion-molecule reactions that can cause false negatives. In this work, we employ HiKE-IMS for the analysis of phenyl-2-propanone (P2P) and other precursor chemicals used for synthesis of methamphetamine and amphetamine. The results show that the precursor chemicals exhibit different behavior in HiKE-IMS. Some precursors form a single significant ion species, while others readily form a fragmentation pattern. Nevertheless, all drug precursors can be distinguished from each other, from the reactant ions and from interfering compounds. In particular, the field-dependent ion mobility as an additional separation dimension aids identification, potentially reducing the number of false positive alarms in field applications. Furthermore, the analysis of a seized illicit P2P sample shows that even low levels of P2P can be detected despite the complex background present in the headspace of real samples.
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Affiliation(s)
- Christoph Schaefer
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstr. 9A, Hannover 30167, Germany.
| | - Martin Lippmann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstr. 9A, Hannover 30167, Germany
| | - Clara Schindler
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstr. 9A, Hannover 30167, Germany
| | - Michiel Beukers
- Research Group Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H Tromplaan 28, Enschede 7513AB, the Netherlands; Knowledge Centre of Digitalization, Intelligence and Technology, Police Academy of the Netherlands, Arnhemseweg 348, Apeldoorn 7334AC, the Netherlands
| | - Niels Beijer
- Research Group Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H Tromplaan 28, Enschede 7513AB, the Netherlands; Knowledge Centre of Digitalization, Intelligence and Technology, Police Academy of the Netherlands, Arnhemseweg 348, Apeldoorn 7334AC, the Netherlands
| | - Moritz Hitzemann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstr. 9A, Hannover 30167, Germany
| | - Ben van de Kamp
- Research Group Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H Tromplaan 28, Enschede 7513AB, the Netherlands; Knowledge Centre of Digitalization, Intelligence and Technology, Police Academy of the Netherlands, Arnhemseweg 348, Apeldoorn 7334AC, the Netherlands
| | - Ruud Peters
- Research Group Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H Tromplaan 28, Enschede 7513AB, the Netherlands; Knowledge Centre of Digitalization, Intelligence and Technology, Police Academy of the Netherlands, Arnhemseweg 348, Apeldoorn 7334AC, the Netherlands
| | - Jaap Knotter
- Research Group Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H Tromplaan 28, Enschede 7513AB, the Netherlands; Knowledge Centre of Digitalization, Intelligence and Technology, Police Academy of the Netherlands, Arnhemseweg 348, Apeldoorn 7334AC, the Netherlands
| | - Stefan Zimmermann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Appelstr. 9A, Hannover 30167, Germany
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3
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Williamson DL, Naylor CN, Nagy G. Sequencing Sialic Acid Positioning in Gangliosides by High-Resolution Cyclic Ion Mobility Separations Coupled with Multiple Collision-Induced Dissociation-Based Tandem Mass Spectrometry Strategies. Anal Chem 2024. [PMID: 39137259 DOI: 10.1021/acs.analchem.4c03411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Gangliosides, a diverse class of glycosphingolipids, are highly abundant in neural tissue and have been implicated in numerous aging-related diseases. Their characterization with methods such as liquid chromatography-tandem mass spectrometry is often precluded by their structural complexity, isomeric heterogeneity, and lack of commercially available authentic standards. In this work, we coupled high-resolution cyclic ion mobility spectrometry with multiple collision-induced dissociation-based tandem mass spectrometry strategies to sequence the sialic acid positions in various ganglioside isomers. Initially, as a proof-of-concept demonstration, we were able to characterize the sialic acid positions in several GD1 and GT1 species. From there, we extended our approach to identify the location of N-glycolylneuraminic acid (NeuGc) residues in previously uncharacterized GD1 and GQ1 isomers. Our results highlight the potential of this presented methodology for the de novo characterization of gangliosides within complex biological matrices without the need for authentic standards.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Cameron N Naylor
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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4
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Yang HC, Scruggs SS, Chai M, Mathai G, Taylor JS, Gross ML. Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1768-1774. [PMID: 38952267 PMCID: PMC11305913 DOI: 10.1021/jasms.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between nonadjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of nonadjacent CPDs of C=T, T=C, and C=C, and successful analysis depends on development of specific and sensitive methods. Toward meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans,anti T=T CPDs. Ion mobility can afford baseline separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers.
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Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Savannah S. Scruggs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Mengqi Chai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - George Mathai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - John-Stephen Taylor
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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5
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Habibi SC, Bradford VR, Baird SC, Lucas SW, Chouinard CD, Nagy G. Development of a cyclic ion mobility spectrometry-mass spectrometry-based collision cross-section database of permethylated human milk oligosaccharides. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5076. [PMID: 39041358 PMCID: PMC11283840 DOI: 10.1002/jms.5076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/28/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024]
Abstract
Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain-gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons - there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High-resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed-phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first-ever high-resolution collision cross-section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high-resolution cyclic ion mobility spectrometry-mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography-tandem mass spectrometry-based methods.
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Affiliation(s)
- Sanaz C. Habibi
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Victoria R. Bradford
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Sophie C. Baird
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Shadrack Wilson Lucas
- Department of Chemistry, Clemson University, Clemson, South Carolina 29625, United States
| | | | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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6
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Su P, Zhu X, Wilson SM, Feng Y, Samayoa-Oviedo HY, Sonnendecker C, Smith AJ, Zimmermann W, Laskin J. The effect of host size on binding in host-guest complexes of cyclodextrins and polyoxometalates. Chem Sci 2024; 15:11825-11836. [PMID: 39092096 PMCID: PMC11290418 DOI: 10.1039/d4sc01061b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/07/2024] [Indexed: 08/04/2024] Open
Abstract
Harnessing flexible host cavities opens opportunities for the design of novel supramolecular architectures that accommodate nanosized guests. This research examines unprecedented gas-phase structures of Keggin-type polyoxometalate PW12O40 3- (WPOM) and cyclodextrins (X-CD, X = α, β, γ, δ, ε, ζ) including previously unexplored large, flexible CDs. Using ion mobility spectrometry coupled to mass spectrometry (IM-MS) in conjunction with molecular dynamics (MD) simulations, we provide first insights into the binding modes between WPOM and larger CD hosts as isolated structures. Notably, γ-CD forms two distinct structures with WPOM through binding to its primary and secondary faces. We also demonstrate that ε-CD forms a deep inclusion complex, which encapsulates WPOM within its annular inner cavity. In contrast, ζ-CD adopts a saddle-like conformation in its complex with WPOM, which resembles its free form in solution. More intriguingly, the gas-phase CD-WPOM structures are highly correlated with their counterparts in solution as characterized by nuclear magnetic resonance (NMR) spectroscopy. The strong correlation between the gas- and solution phase structures of CD-WPOM complexes highlight the power of gas-phase IM-MS for the structural characterization of supramolecular complexes with nanosized guests, which may be difficult to examine using conventional approaches.
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Affiliation(s)
- Pei Su
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Xiao Zhu
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
- Rosen Center for Advanced Computing, Purdue University West Lafayette Indiana 47907 USA
| | - Solita M Wilson
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Yuanning Feng
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
- Department of Chemistry and Biochemistry, The University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
| | - Hugo Y Samayoa-Oviedo
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Christian Sonnendecker
- Institute of Analytical Chemistry, Universität Leipzig Johannisallee 29 Leipzig 04103 Germany
| | - Andrew J Smith
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Wolfgang Zimmermann
- Institute of Analytical Chemistry, Universität Leipzig Johannisallee 29 Leipzig 04103 Germany
| | - Julia Laskin
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
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7
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Duez Q, van de Wiel J, van Sluijs B, Ghosh S, Baltussen MG, Derks MTGM, Roithová J, Huck WTS. Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry. J Am Chem Soc 2024; 146:20778-20787. [PMID: 39013149 PMCID: PMC11295183 DOI: 10.1021/jacs.4c04218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.
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Affiliation(s)
| | | | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Souvik Ghosh
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Max T. G. M. Derks
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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8
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Rudt E, Schneider S, Hayen H. Hyphenation of Liquid Chromatography and Trapped Ion Mobility - Mass Spectrometry for Characterization of Isomeric Phosphatidylethanolamines with Focus on N-Acylated Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1584-1593. [PMID: 38842006 DOI: 10.1021/jasms.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
In prior research, hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry (HILIC-MS/MS) has demonstrated applicability for characterizing regioisomers in lipidomics studies, including phosphatidylglycerols (PG) and bis(monoacyl)glycerophosphates (BMP). However, there are other lipid regioisomers, such as phosphatidylethanolamines (PE) and lyso-N-acyl-PE (LNAPE), that have not been studied as extensively. Therefore, hyphenated mass spectrometric methods are needed to investigate PE and LNAPE regioisomers individually. The asymmetric structure of LNAPE favors isomeric species, which can result in coelution and chimeric MS/MS spectra. One way to address the challenge of chimeric MS/MS spectra is through mobility-resolved fragmentation using trapped ion mobility spectrometry (TIMS). Therefore, we developed a multidimensional HILIC-TIMS-MS/MS approach for the structural characterization of isomeric phosphatidylethanolamines in both negative and positive ionization modes. The study revealed the complementary fragmentation pattern and ion mobility behavior of LNAPE in both ionization modes, which was confirmed by a self-synthesized LNAPE standard. With this knowledge, a distinction of regioisomeric PE and LNAPE was achieved in human plasma samples. Furthermore, regioisomeric LNAPE species containing at least one unsaturated fatty acid were noted to exhibit a change in collision cross-section in positive ionization mode, leading to a lipid characterization with respect to fatty acyl positional level. Similar mobility behavior was also observed for the biological LNAPE precursor N-acyl-PE (NAPE). Application of this approach to plasma and cereal samples demonstrated its effectiveness in regioisomeric LNAPE and NAPE species' elucidation.
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Affiliation(s)
- Edward Rudt
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, Münster 48149, Germany
| | - Svenja Schneider
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, Münster 48149, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, Münster 48149, Germany
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9
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Höving S, Schomacher J, Schiller A, Franzke J. Setting the Separation Factor α for Ketone Monomers and Dimers by the Use of Different Drift Gases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1622-1628. [PMID: 38866725 DOI: 10.1021/jasms.4c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
This study investigates the influence of different drift gases on ion mobility in ion mobility spectrometry (IMS) using ketones as model substances within a custom-built drift tube spectrometer. Different binary mixtures of nitrogen, helium, and argon were used as drift gases to investigate the influence of mobility on the monomers and dimers of the different ketones. Experimental results reveal shifts in ion drift times and separation factors (α) with varying gas compositions, in accordance with Blanc's Law. Furthermore, the study underscores the device-independent nature of α and the device-dependent resolution, emphasizing the importance of comparative analyses. Employing 2-hexanone and 2-decanone in the same sample but with different drift gases is used to show the impact of different drift gases. By changing the drift gas composition, total alignment of drift times and therefore no possible resolution or baseline resolution could be achieved. Through different experiments and analyses, this research provides insights into the interactions between gas composition and ion mobility, offering implications for diverse analytical applications from environmental monitoring to chemical detection.
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Affiliation(s)
- Simon Höving
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Jos Schomacher
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Arthur Schiller
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
| | - Joachim Franzke
- Miniaturisation, Leibniz-Institut für Analytische Wissenschaften ISAS e.V., 44139 Dortmund, Germany
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10
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Kwantwi-Barima P, Hollerbach AL, Attah IK, Norheim RV, Ibrahim YM. Ion Mobility Separations Using Cocentric Architecture. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1576-1583. [PMID: 38859729 DOI: 10.1021/jasms.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Ion mobility separations, especially using drift tube ion mobility spectrometers, are usually performed in linear channels, which can have a large footprint when extended to achieve higher resolving powers. In this work, we explored the performance of an ion mobility device with a curved architecture, which can have a more compact form. The cocentric ion mobility spectrometer (CoCIMS) manipulates ions between two cocentric surfaces containing a serpentine track. The mobility separation inside the CoCIMS is achieved using traveling waveforms (TWs). We initially evaluated the device using ion trajectory simulations using SIMION, which indicated that when ions traveled circularly inside the CoCIMS they resulted in similar resolving powers and transmitted m/z range as traveling in a straight path. We then performed experimental validation of the CoCIMS in conjunction with a TOF MS. The CoCIMS was made of two flexible printed circuit board materials folded into cocentric cylinders separated by a gap of 2.8 mm. The device was about 50 mm diameter ×152 mm long and provided 1.846 m of serpentine path length. Three sets of mixtures (Agilent tune mixture, tetraalkylammonium salts, and an eight-peptide mixture) and four traveling waveform profiles (square, sine, triangle, and sawtooth) were used. The sawtooth TW profile produced a slightly higher resolving power for the Agilent tuning mixture and tetraalkylammonium ions. The average resolving power for Agilent tune mixture ions ranged from 37 (using sawtooth TW) to 27 (using square TW). The average resolving powers ranged from 45 (sawtooth TW) to 31 (square TW) for tetraalkylammonium ions. The resolving power of the peptide mixture ions was similar among the four TW profiles and ranged from 51 to 56. The average percent error in TWCCS for the peptide mixture ions was about 0.4%. The new device showed promising results, but improvements are needed to further increase the resolving power.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Randolph V Norheim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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11
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Polewski L, Moon E, Zappe A, Götze M, Szekeres GP, Roth C, Pagel K. Ion Mobility Mass Spectrometry-Based Disaccharide Analysis of Glycosaminoglycans. Chemistry 2024; 30:e202400783. [PMID: 38629399 DOI: 10.1002/chem.202400783] [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: 02/26/2024] [Indexed: 05/24/2024]
Abstract
Glycosaminoglycans (GAGs) are linear and acidic polysaccharides. They are ubiquitous molecules, which are involved in a wide range of biological processes. Despite being structurally simple at first glance, with a repeating backbone of alternating hexuronic acid and hexosamine dimers, GAGs display a highly complex structure, which predominantly results from their heterogeneous sulfation patterns. The commonly applied method for compositional analysis of all GAGs is "disaccharide analysis." In this process, GAGs are enzymatically depolymerized into disaccharides, derivatized with a fluorescent label, and then analysed through liquid chromatography. The limiting factor in the high throughput analysis of GAG disaccharides is the time-consuming liquid chromatography. To address this limitation, we here utilized trapped ion mobility-mass spectrometry (TIM-MS) for the separation of isomeric GAG disaccharides, which reduces the measurement time from hours to a few minutes. A full set of disaccharides comprises twelve structures, with eight possessing isomers. Most disaccharides cannot be differentiated by TIM-MS in underivatized form. Therefore, we developed chemical modifications to reduce sample complexity and enhance differentiability. Quantification is performed using stable isotope labelled standards, which are easily available due to the nature of the performed modifications.
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Affiliation(s)
- Lukasz Polewski
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
- Department of Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195, Berlin, Faradayweg 4-6, Germany
| | - Eunjin Moon
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
| | - Andreas Zappe
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
| | - Michael Götze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
- Department of Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195, Berlin, Faradayweg 4-6, Germany
| | - Gergo Peter Szekeres
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
- Department of Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195, Berlin, Faradayweg 4-6, Germany
| | - Christian Roth
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, 14195, Berlin, Arnimallee 22, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Altensteinstraße 23a, Germany
- Department of Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195, Berlin, Faradayweg 4-6, Germany
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12
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Williams-Pavlantos K, Mokarizadeh AH, Curole BJ, Grayson SM, Tsige M, Wesdemiotis C. Elucidation of Dithiol-yne Comb Polymer Architectures by Tandem Mass Spectrometry and Ion Mobility Techniques. Polymers (Basel) 2024; 16:1665. [PMID: 38932016 PMCID: PMC11207239 DOI: 10.3390/polym16121665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymers have a wide range of applications depending on their composition, size, and architecture. Varying any of these three characteristics can greatly impact the resulting chemical, physical, and mechanical properties. While many techniques are available to determine polymer composition and size, determining the exact polymer architecture is more challenging. Herein, tandem mass spectrometry (MS/MS) and ion mobility mass spectrometry (IM-MS) methods are utilized to derive crucial architectural information about dithiol-yne comb polymers. Based on their unique fragmentation products and IM drift times, dithiol-yne oligomers with distinct architectures were successfully differentiated and characterized. Additionally, experimental collision cross-sections (Ω) derived via IM-MS were compared to theoretically extracted Ω values from molecular dynamics simulated structures to deduce the architectural motif of these comb oligomers. Overall, this work demonstrates the benefits of combining various mass spectrometry techniques in order to gain a complete understanding of a complex polymer mixture.
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Affiliation(s)
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Brennan J. Curole
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Scott M. Grayson
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA;
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
| | - Chrys Wesdemiotis
- Department of Chemistry, University of Akron, Akron, OH 44325, USA;
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH 44325, USA; (A.H.M.); (M.T.)
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13
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Zangl R, Soravia S, Saft M, Löffler JG, Schulte J, Rosner CJ, Bredenbeck J, Essen LO, Morgner N. Time-Resolved Ion Mobility Mass Spectrometry to Solve Conformational Changes in a Cryptochrome. J Am Chem Soc 2024; 146:14468-14478. [PMID: 38757172 DOI: 10.1021/jacs.3c13818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Many biological mechanisms rely on the precise control of conformational changes in proteins. Understanding such dynamic processes requires methods for determining structures and their temporal evolution. In this study, we introduce a novel approach to time-resolved ion mobility mass spectrometry. We validated the method on a simple photoreceptor model and applied it to a more complex system, the animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY), to determine the role of specific amino acids affecting the conformational dynamics as reaction to blue light activation. In our setup, using a high-power LED mounted in the source region of an ion mobility mass spectrometer, we allow a time-resolved evaluation of mass and ion mobility spectra. Cryptochromes like CraCRY are a widespread type of blue light photoreceptors and mediate various light-triggered biological functions upon excitation of their inbuilt flavin chromophore. Another hallmark of cryptochromes is their flexible carboxy-terminal extension (CTE), whose structure and function as well as the details of its interaction with the photolyase homology region are not yet fully understood and differ among different cryptochromes types. Here, we addressed the highly conserved C-terminal domain of CraCRY, to study the effects of single mutations on the structural transition of the C-terminal helix α22 and the attached CTE upon lit-state formation. We show that D321, the putative proton acceptor of the terminal proton-coupled electron transfer event from Y373, is essential for triggering the large-scale conformational changes of helix α22 and the CTE in the lit state, while D323 influences the timing.
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Affiliation(s)
- Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Sejla Soravia
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
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14
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George AC, Schmitz I, Rouvière F, Alves S, Colsch B, Heinisch S, Afonso C, Fenaille F, Loutelier-Bourhis C. Interplatform comparison between three ion mobility techniques for human plasma lipid collision cross sections. Anal Chim Acta 2024; 1304:342535. [PMID: 38637036 DOI: 10.1016/j.aca.2024.342535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The implementation of ion mobility spectrometry (IMS) in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) workflows has become a valuable tool for improving compound annotation in metabolomics analyses by increasing peak capacity and by adding a new molecular descriptor, the collision cross section (CCS). Although some studies reported high repeatability and reproducibility of CCS determination and only few studies reported good interplatform agreement for small molecules, standardized protocols are still missing due to the lack of reference CCS values and reference materials. We present a comparison of CCS values of approximatively one hundred lipid species either commercially available or extracted from human plasma. We used three different commercial ion mobility technologies from different laboratories, drift tube IMS (DTIMS), travelling wave IMS (TWIMS) and trapped IMS (TIMS), to evaluate both instrument repeatability and interlaboratory reproducibility. We showed that CCS discrepancies of 0.3% (average) could occur depending on the data processing software tools. Moreover, eleven CCS calibrants were evaluated yielding mean RSD below 2% for eight calibrants, ESI Low concentration tuning mix (Tune Mix) showing the lowest RSD (< 0.5%) in both ion modes. Tune Mix calibrated CCS from the three different IMS instruments proved to be well correlated and highly reproducible (R2 > 0.995 and mean RSD ≤ 1%). More than 90% of the lipid CCS had deviations of less than 1%, demonstrating high comparability between techniques, and the possibility to use the CCS as molecular descriptor. We highlighted the need of standardized procedures for calibration, data acquisition, and data processing. This work demonstrates that using harmonized analytical conditions are required for interplatform reproducibility for CCS determination of human plasma lipids.
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Affiliation(s)
- Anaïs C George
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Isabelle Schmitz
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - Florent Rouvière
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Sabine Heinisch
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Carlos Afonso
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France
| | - Corinne Loutelier-Bourhis
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000, Rouen, France.
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15
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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16
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Benzenberg LR, Katzberger P, Wu R, Metternich JB, Riniker S, Zenobi R. Probing the Stability of a β-Hairpin Scaffold after Desolvation. J Phys Chem Lett 2024; 15:5041-5046. [PMID: 38700091 DOI: 10.1021/acs.jpclett.4c00920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Probing the structural characteristics of biomolecular ions in the gas phase following native mass spectrometry (nMS) is of great interest, because noncovalent interactions, and thus native fold features, are believed to be largely retained upon desolvation. However, the conformation usually depends heavily on the charge state of the species investigated. In this study, we combine transition metal ion Förster resonance energy transfer (tmFRET) and ion mobility-mass spectrometry (IM-MS) with molecular dynamics (MD) simulations to interrogate the β-hairpin structure of GB1p in vacuo. Fluorescence lifetime values and collisional cross sections suggest an unfolding of the β-hairpin motif for higher charge states. MD simulations are consistent with experimental constraints, yet intriguingly provide an alternative structural interpretation: preservation of the β-hairpin is not only predicted for 2+ but also for 4+ charged species, which is unexpected given the substantial Coulomb repulsion for small secondary structure scaffolds.
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Affiliation(s)
- Lukas R Benzenberg
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Paul Katzberger
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ri Wu
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Jonas B Metternich
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sereina Riniker
- Institute of Molecular Physical Science, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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17
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Zimnicka MM. Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:526-559. [PMID: 37260128 DOI: 10.1002/mas.21851] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.
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Affiliation(s)
- Magdalena M Zimnicka
- Mass Spectrometry Group, Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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18
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Webb IK. Perspective: The complex relationship between charge, mobility, and gas-phase protein structure. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5013. [PMID: 38605450 DOI: 10.1002/jms.5013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Ion mobility spectrometry coupled to mass spectrometry (IMS/MS) is a widely used tool for biomolecular separations and structural elucidation. The application of IMS/MS has resulted in exciting developments in structural proteomics and genomics. This perspective gives a brief background of the field, addresses some of the important issues in making structural measurements, and introduces complementary techniques.
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Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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19
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Wesdemiotis C, Williams-Pavlantos KN, Keating AR, McGee AS, Bochenek C. Mass spectrometry of polymers: A tutorial review. MASS SPECTROMETRY REVIEWS 2024; 43:427-476. [PMID: 37070280 DOI: 10.1002/mas.21844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Ever since the inception of synthetic polymeric materials in the late 19th century, the number of studies on polymers as well as the complexity of their structures have only increased. The development and commercialization of new polymers with properties fine-tuned for specific technological, environmental, consumer, or biomedical applications requires powerful analytical techniques that permit the in-depth characterization of these materials. One such method with the ability to provide chemical composition and structure information with high sensitivity, selectivity, specificity, and speed is mass spectrometry (MS). This tutorial review presents and exemplifies the various MS techniques available for the elucidation of specific structural features in a synthetic polymer, including compositional complexity, primary structure, architecture, topology, and surface properties. Key to every MS analysis is sample conversion to gas-phase ions. This review describes the fundamentals of the most suitable ionization methods for synthetic materials and provides relevant sample preparation protocols. Most importantly, structural characterizations via one-step as well as hyphenated or multidimensional approaches are introduced and demonstrated with specific applications, including surface sensitive and imaging techniques. The aim of this tutorial review is to illustrate the capabilities of MS for the characterization of large, complex polymers and emphasize its potential as a powerful compositional and structural elucidation tool in polymer chemistry.
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Affiliation(s)
| | | | - Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Andrew S McGee
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Calum Bochenek
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
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20
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Brodmerkel MN, Thiede L, De Santis E, Uetrecht C, Caleman C, Marklund EG. Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Phys Chem Chem Phys 2024; 26:13094-13105. [PMID: 38628116 DOI: 10.1039/d3cp06344e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
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21
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Williamson DL, Windsor HM, Nagy G. Isolating the Contributions from Moments of Inertia in Isotopic Shifts Measured by High-Resolution Cyclic Ion Mobility Separations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38654703 DOI: 10.1021/jasms.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The unexpected finding that isotopomers (i.e., isotopic isomers) can be separated with high-resolution ion mobility spectrometry-mass spectrometry (IMS-MS) has raised new structural considerations affecting an ion's mobility, namely its center of mass (CoM) and moments of inertia (MoI). Unfortunately, thus far, no studies have attempted to experimentally isolate either CoM or MoI, as they are intrinsically linked by their definitions, where MoI is calculated in relation to CoM. In this study, we designed and synthesized four isotopically labeled tetrapropylammonium (TAA3) ions, each with a unique mass distribution. Three of the synthesized TAA3 ions were labeled symmetrically, thus having identical CoM but differing MoI, which we verified using density functional theory (DFT) calculations. Consequently, we were able to isolate the effect of MoI changes in high-resolution IMS-MS separations. Cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS) separations of the isotopically labeled TAA3 variants revealed isotopic mobility shifts attributable solely to changes in MoI. A 60-m cIMS-MS separation demonstrated that two nominally isobaric TAA3 pseudoisotopomers could be partially resolved, showcasing potential feasibility for isotopomer separations on commercially available IMS-MS platforms. With our previously established collision cross section (CCS) calibration protocol, we also quantified the relationship between MoI and CCS. Our results represent the first demonstration of IMS-MS separations based solely on MoI differences. We believe these findings will contribute important evidence to the growing body of literature on the physical nature of isotopic shifts in IMS-MS separations and work toward more accurate CCS predictions.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Haisley M Windsor
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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22
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Zhu B, An H, Li L, Zhang H, Lv J, Hu W, Xue F, Liu L, He S, Li D. Characterization of Flavor Profiles of Cigar Tobacco Leaves Grown in China via Headspace-Gas Chromatography-Ion Mobility Spectrometry Coupled with Multivariate Analysis and Sensory Evaluation. ACS OMEGA 2024; 9:15996-16005. [PMID: 38617669 PMCID: PMC11007687 DOI: 10.1021/acsomega.3c09499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Although cigar tobacco leaves (CTLs) have a high economic value, research regarding the flavor characteristics of CTLs is currently limited. A comprehensive study of the flavor characteristics of CTLs from different regions of China was conducted by identifying their volatile-flavor-containing compounds (VFCs) and flavors. The samples were analyzed via gas chromatography-ion mobility spectrometry (GC-IMS) and sensory evaluation. Results revealed considerable differences in the VFC contents of CTLs from different regions of China, suggesting that the VFLs of CTLs could be influenced by geographical origin. Mainly, phenols, pyrazines, and aldehydes were present in the CTLs from Sichuan. High contents of esters and pyrazines were present in the CTLs from Hubei, while esters were the major components of the CTLs from Hainan. Multivariate analysis results showed the effective differentiation of samples from different geographical origins based on the GC-IMS results. Sensory evaluation revealed that the flavors of CTLs from different geographical origins were different. 1,8-Pinene, 3-methyl-3-butene-1-ol, 2,3-dimethyl-5-ethylpyrazine, 4-methyl-3-penten-2-one, and (E)-2-pentenal might serve as geographical marker compounds, indicating the geographical origin of CTLs based on the results of GC-IMS and sensory evaluation. This study may be beneficial for the trade of CTLs and the development of cigar products.
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Affiliation(s)
- Beibei Zhu
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Hongyue An
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Li Li
- Technology
Center, China Tobacco Sichuan Industrial
Co., Ltd., No. 80, Fourth
Road, Section 1 of Checheng West, Longquan District, Chengdu 610100, China
| | - Hongfei Zhang
- National
Tobacco Quality Supervision and Test Center, No. 6, Green Bamboo Street, New
and High-Tech Industrial Development District, Zhengzhou 450001, China
| | - Jinxiong Lv
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Wanrong Hu
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Fang Xue
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Lulu Liu
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
| | - Shengbao He
- National
Tobacco Quality Supervision and Test Center, No. 6, Green Bamboo Street, New
and High-Tech Industrial Development District, Zhengzhou 450001, China
| | - Dongliang Li
- Key
Laboratory of Chinese Cigar Fermentation, China Tobacco Technology
Innovation Center for Cigar, China Tobacco
Sichuan Industrial Co., Ltd., No. 80, Fourth Road, Section 1 of Checheng West,
Longquan District, Chengdu 610100, China
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23
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Wang N, Dixit SM, Lee T, DeFiglia SA, Ruotolo BT, Håkansson K. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:784-792. [PMID: 38489759 DOI: 10.1021/jasms.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD.
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Affiliation(s)
- Ning Wang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Teresa Lee
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Steven A DeFiglia
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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24
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Charalampidou A, Nehls T, Meyners C, Gandhesiri S, Pomplun S, Pentelute BL, Lermyte F, Hausch F. Automated Flow Peptide Synthesis Enables Engineering of Proteins with Stabilized Transient Binding Pockets. ACS CENTRAL SCIENCE 2024; 10:649-657. [PMID: 38559286 PMCID: PMC10979424 DOI: 10.1021/acscentsci.3c01283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024]
Abstract
Engineering at the amino acid level is key to enhancing the properties of existing proteins in a desired manner. So far, protein engineering has been dominated by genetic approaches, which have been extremely powerful but only allow for minimal variations beyond the canonical amino acids. Chemical peptide synthesis allows the unrestricted incorporation of a vast set of unnatural amino acids with much broader functionalities, including the incorporation of post-translational modifications or labels. Here we demonstrate the potential of chemical synthesis to generate proteins in a specific conformation, which would have been unattainable by recombinant protein expression. We use recently established rapid automated flow peptide synthesis combined with solid-phase late-stage modifications to rapidly generate a set of FK506-binding protein 51 constructs bearing defined intramolecular lactam bridges. This trapped an otherwise rarely populated transient pocket-as confirmed by crystal structures-which led to an up to 39-fold improved binding affinity for conformation-selective ligands and represents a unique system for the development of ligands for this rare conformation. Overall, our results show how rapid automated flow peptide synthesis can be applied to precision protein engineering.
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Affiliation(s)
- Anna Charalampidou
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Thomas Nehls
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
| | - Satish Gandhesiri
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sebastian Pomplun
- Leiden
Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frederik Lermyte
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
| | - Felix Hausch
- Clemens-Schöpf-Institute,
Department of Chemistry, Technical University
of Darmstadt, Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany
- Department
of Synthetic Biology, Technical University
of Darmstadt, 64287 Darmstadt, Germany
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25
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Schweipert M, Nehls T, Frühauf A, Debarnot C, Kumar A, Knapp S, Lermyte F, Meyer‐Almes F. The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation. Protein Sci 2024; 33:e4917. [PMID: 38358265 PMCID: PMC10868454 DOI: 10.1002/pro.4917] [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: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Human histone deacetylase 4 (HDAC4) is a key epigenetic regulator involved in a number of important cellular processes. This makes HDAC4 a promising target for the treatment of several cancers and neurodegenerative diseases, in particular Huntington's disease. HDAC4 is highly regulated by phosphorylation and oxidation, which determine its nuclear or cytosolic localization, and exerts its function through multiple interactions with other proteins, forming multiprotein complexes of varying composition. The catalytic domain of HDAC4 is known to interact with the SMRT/NCOR corepressor complex when the structural zinc-binding domain (sZBD) is intact and forms a closed conformation. Crystal structures of the HDAC4 catalytic domain have been reported showing an open conformation of HDAC4 when bound to certain ligands. Here, we investigated the relevance of this HDAC4 conformation under physiological conditions in solution. We show that proper zinc chelation in the sZBD is essential for enzyme function. Loss of the structural zinc ion not only leads to a massive decrease in enzyme activity, but it also has serious consequences for the overall structural integrity and stability of the protein. However, the Zn2+ free HDAC4 structure in solution is incompatible with the open conformation. In solution, the open conformation of HDAC4 was also not observed in the presence of a variety of structurally divergent ligands. This suggests that the open conformation of HDAC4 cannot be induced in solution, and therefore cannot be exploited for the development of HDAC4-specific inhibitors.
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Affiliation(s)
- Markus Schweipert
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Thomas Nehls
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Anton Frühauf
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Cecilé Debarnot
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Adarsh Kumar
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Stefan Knapp
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Frederik Lermyte
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Franz‐Josef Meyer‐Almes
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
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26
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 DOI: 10.3390/cells13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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27
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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. SCIENCE ADVANCES 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] [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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28
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Das S, Merz KM. Molecular Gas-Phase Conformational Ensembles. J Chem Inf Model 2024; 64:749-760. [PMID: 38206321 DOI: 10.1021/acs.jcim.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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29
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Kwantwi-Barima P, Garimella SVB, Attah IK, Zheng X, Ibrahim YM, Smith RD. Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:365-377. [PMID: 38175933 PMCID: PMC10853970 DOI: 10.1021/jasms.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/19/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of "in-SLIM" ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a "gate" for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit, and the spatial distributions of accumulated ions examined. The ion populations for a set of peptides increased approximately linearly with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ion activation increased with added storage times and the TW amplitude. Lower amplitude TWs in the accumulation/storage region prevented or minimized ion losses or ion heating effects that can also lead to fragmentation. Our results supported the use of an accumulation region close to the SLIM entrance for speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and are ordered in the SLIM based on their mobilities. Only the highest mobility ions located closest to the gate in the trapped ion population (and where the highest ion densities were achieved) were significantly activated. The observed separations may offer utility for ion prefractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefiting from separations of extremely large ion populations.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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30
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Mubas-Sirah F, Gandhi VD, Latif M, Hua L, Tootchi A, Larriba-Andaluz C. Ion mobility calculations of flexible all-atom systems at arbitrary fields using two-temperature theory. Phys Chem Chem Phys 2024; 26:4118-4124. [PMID: 38226667 DOI: 10.1039/d3cp05415b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Ion mobility spectrometry (IMS) separates and analyzes ions based on their mobility in a gas under an electric field. When the field is increased, the mobility varies in a complex way that depends on the relative velocity between gas and ion, their electrostatic potential interactions, and the effects from direct impingement. Recently, the two-temperature theory, primarily developed for monoatomic ions in monoatomic gases, has been extended to study mobilities at arbitrary fields using polyatomic ions in polyatomic gases, with some success. However, this extension poses challenges, such as inelastic collisions between gas and ion and structural modifications of ions as they heat up. These challenges become significant when working with diatomic gases and flexible molecules. In a previous study, experimental mobilities of tetraalkylammonium salts were obtained using a FAIMS instrument, showing satisfactory agreement with numerical two-temperature theory predictions. However, deviations occurred at fields greater than 100 Td. To address this issue, this paper introduces a modified high-field calculation method that accounts for the structural changes in ions due to field heating. The study focuses on tetraheptylammonium (THA+), tetradecylammonium (TDA+), and tetradodecylammonium (TDDA+) salts. Molecular structures were generated at various temperatures using MM2 forcefield. The mobility was calculated using IMoS 1.13 with two-temperature trajectory method calculations up to the fourth approximation. Multiple effective temperatures were considered, and a linear weighing system was used to create mobility vs. reduced field strength plots. The results suggest that the structural enlargement due to ion heating plays a significant role in mobility at high fields, aligning better with experimental data. FAIMS' dispersion plots also show improved agreement with experimental results. However, the contribution of inelastic collisions and energy transfer to rotational degrees of freedom in gas molecules remains a complex and challenging aspect.
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Affiliation(s)
- Farah Mubas-Sirah
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Viraj D Gandhi
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
- Department of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
| | - Mohsen Latif
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Leyan Hua
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Amirreza Tootchi
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
| | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA.
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31
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Wu R, Svingou D, Metternich JB, Benzenberg LR, Zenobi R. Transition Metal Ion FRET-Based Probe to Study Cu(II)-Mediated Amyloid- β Ligand Binding. J Am Chem Soc 2024; 146:2102-2112. [PMID: 38225538 DOI: 10.1021/jacs.3c11533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Recent therapeutic strategies suggest that small peptides can act as aggregation inhibitors of monomeric amyloid-β (Αβ) by inducing structural rearrangements upon complexation. However, characterizing the binding events in such dynamic and transient noncovalent complexes, especially in the presence of natively occurring metal ions, remains a challenge. Here, we deploy a combined transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) approach to characterize the structure of mass- and charge-selected Aβ complexes with Cu(II) ions (a quencher) and a potential aggregation inhibitor, a small neuropeptide named leucine enkephalin (LE). We show conformational changes of monomeric Αβ species upon Cu(II)-binding, indicating an uncoiled N-terminus and a close interaction between the C-terminus and the central hydrophobic region. Furthermore, we introduce LE labeled at the N-terminus with a metal-chelating agent, nitrilotriacetic acid (NTA). This allows us to employ tmFRET to probe the binding even in low-abundance and transient Aβ-inhibitor-metal ion complexes. Complementary intramolecular distance and global shape information from tmFRET and native IM-MS, respectively, confirmed Cu(II) displacement toward the N-terminus of Αβ, which discloses the binding region and the inhibitor's orientation.
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Affiliation(s)
- Ri Wu
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Despoina Svingou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonas B Metternich
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Lukas R Benzenberg
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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32
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Zercher BP, Feng Y, Bush MF. Towards IM n with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Ion Mobility. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117163. [PMID: 37928050 PMCID: PMC10621600 DOI: 10.1016/j.ijms.2023.117163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Increasing the dimensionality of ion mobility (IM) presents an enticing opportunity to increase the information content and selectivity of many analyses. However, for implementations of IM that use constant electrostatic gradients to separate ions in a buffer gas, technical challenges have limited the adoption of the technique and number of dimensions within individual experiments. Here, we introduce a strategy to "reset" the potentials of ions between IM dimensions. To achieve this, mobility-selected ions are trapped between dimensions of IM, using a combination of RF and electrostatic fields, while the subsequent dimension of IM is devoid of any drift field. By applying an incremental voltage ramp, the potential of the trapping region is elevated, simultaneously establishing the drift field in the subsequent dimension of IM. The trapped ions are then released and separated. We measured similar arrival-time distributions of protein ions using this strategy and a method without potential resetting, suggesting that potential resetting can be performed without additional losses or activation of ions. The findings of those experiments were corroborated by ion trajectory simulations, which exhibited a very small changes in ion position and no significant changes in effective temperatures during potential resetting. Finally, we demonstrate that IM information can be preserved during potential resetting by selecting subpopulations of 9+ cytochrome c ions, resetting their potential, subjecting them to a second-dimension IM separation, and observing the retention of conformers within each subpopulation. We anticipate that this strategy will be useful for advancing flexible, multidimensional experiments on electrostatic IM instruments.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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33
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Duez Q, Marek L, Váňa J, Hanusek J, Roithová J. Autocatalysis in Eschenmoser Coupling Reactions. Chemistry 2023:e202303619. [PMID: 38088237 DOI: 10.1002/chem.202303619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 12/22/2023]
Abstract
The Eschenmoser coupling reaction (ECR) of thioamides with electrophiles is believed to proceed via thiirane intermediates. However, little is known about converting the intermediates into ECR products. Previous mechanistic studies involved external thiophiles to remove the sulfur atom from the intermediates. In this work, an ECR proceeding without any thiophilic agent or base is studied by electrospray ionization-mass spectrometry. ESI-MS enables the detection of the so-far elusive polysulfide species Sn , with n ranging from 2 to 16 sulfur atoms, proposed to be the key species leading to product formation. Integrating observations from ion mobility spectrometry, ion spectroscopy, and reaction monitoring via flow chemistry coupled with mass spectrometry provides a comprehensive understanding of the reaction mechanism and uncovers the autocatalytic nature of the ECR reaction.
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Affiliation(s)
- Quentin Duez
- Institute for Molecules and Materials, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lukáš Marek
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jiří Váňa
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jiří Hanusek
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ532 10, Pardubice, The Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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34
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Abdulbagi M, Di B, Li B. Resolving D-Amino Acid Containing Peptides Using Ion Mobility-Mass Spectrometry: Challenges and Recent Developments. Crit Rev Anal Chem 2023:1-10. [PMID: 37975700 DOI: 10.1080/10408347.2023.2282510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Peptides and proteins having D-amino acids in their sequences are now believed to be widespread among different living organisms. Their significance is attributed to the diverse functions of these molecules, such as having a certain pathological implication or enhancing biological activity. Indeed, some peptide molecules with D-amino acids in their structure have already found their way to clinical use such as the antibacterial gramicidin and the antidiabetic nateglinide. Ion mobility mass spectrometry (IM-MS) added an additional dimension of separation as it depends on ions mobility in the space, which is dependent on their shapes, and the shape depends on the orientation of atoms. Thus, D-amino acids containing peptides (DAACPs) will have different mobility and collision cross-section values than those with L-amino acids. Eventually, this will lead to baseline separation of the two peptides. Additionally, ion mobility can precisely locate the position of D-amino acids by analyzing the difference in the arrival times of the fragment ions. The importance of DAACPs, as well as the difficulties in discovering them, were addressed in this review. Similarly, we emphasized how recent developments in IM-MS have improved their detection and analysis. Consequently, the LC-IM-MS/MS platform appears to be promising in isomeric mixture analysis.
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Affiliation(s)
- Mohamed Abdulbagi
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
| | - Bin Di
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Bo Li
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
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35
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Will A, Oliinyk D, Bleiholder C, Meier F. Peptide collision cross sections of 22 post-translational modifications. Anal Bioanal Chem 2023; 415:6633-6645. [PMID: 37758903 PMCID: PMC10598134 DOI: 10.1007/s00216-023-04957-4] [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: 12/23/2022] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
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Affiliation(s)
- Andreas Will
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Denys Oliinyk
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
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36
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Neal SP, Hodges WN, Velosa DC, Aderorho R, Lucas SW, Chouinard CD. Improved analysis of derivatized steroid hormone isomers using ion mobility-mass spectrometry (IM-MS). Anal Bioanal Chem 2023; 415:6757-6769. [PMID: 37740752 DOI: 10.1007/s00216-023-04953-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/25/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023]
Abstract
Over the last decade, applications of ion mobility-mass spectrometry (IM-MS) have exploded due primarily to the widespread commercialization of robust instrumentation from several vendors. Unfortunately, the modest resolving power of many of these platforms (~40-60) has precluded routine separation of constitutional and stereochemical isomers. While instrumentation advances have pushed resolving power to >150 in some cases, chemical approaches offer an alternative for increasing resolution with existing IM-MS instrumentation. Herein we explore the utility of two reactions, derivatization by Girard's reagents and 1,1-carbonyldiimidazole (CDI), for improving IM separation of steroid hormone isomers. These reactions are fast (≤30 min), simple (requiring only basic lab equipment/expertise), and low-cost. Notably, these reactions are structurally selective in that they target carbonyl and hydroxyl groups, respectively, which are found in all naturally occurring steroids. Many steroid hormone isomers differ only in the number, location, and/or stereochemistry of these functional groups, allowing these reactions to "amplify" subtle structural differences and improve IM resolution. Our results show that resolution was significantly improved amongst CDI-derivatized isomer groups of hydroxyprogesterone (two-peak resolution of Rpp = 1.10 between 21-OHP and 11B-OHP), deoxycortisone (Rpp = 1.47 between 11-DHC and 21-DOC), and desoximetasone (Rpp = 1.98 between desoximetasone and fluocortolone). Moreover, characteristic collision cross section (DTCCSN2) measurements can be used to increase confidence in the identification of these compounds in complex biological mixtures. To demonstrate the feasibility of analyzing the derivatized steroids in complex biological matrixes, the reactions were performed following steroid extraction from urine and yielded similar results. Additionally, we applied a software-based approach (high-resolution demultiplexing) that further improved the resolving power (>150). Overall, our results suggest that targeted derivatization reactions coupled with IM-MS can significantly improve the resolution of challenging isomer groups, allowing for more accurate and efficient analysis of complex mixtures.
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Affiliation(s)
- Shon P Neal
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Walker N Hodges
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA
| | - Diana C Velosa
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Ralph Aderorho
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA
| | - Shadrack Wilson Lucas
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA
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Kim J, Tijing L, Shon HK, Hong S. Electrically conductive membrane distillation via an alternating current operation for zero liquid discharge. WATER RESEARCH 2023; 244:120510. [PMID: 37634460 DOI: 10.1016/j.watres.2023.120510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/29/2023]
Abstract
Membrane distillation (MD) shows promise for achieving high salinity treatment and zero liquid discharge (ZLD) compared to conventional water treatment processes due to its unique characteristics, including low energy consumption and high resulting water quality. However, performance degradation due to fouling and scaling under high recovery conditions remains a challenge, particularly considering the need to control both cations and anions for maximum scaling mitigation. Accordingly, in this study, alternating current (AC) operation for electrically conductive membrane distillation (ECMD) is newly proposed, based on its potential for controlling both cations and anions, in contrast to conventional direct current (DC) operation. Systematic experiments and theoretical analysis show that water recovery in ECMD can be increased by 27% through AC operation. The proposed modification and effective AC operation of ECMD increase the practicality of using MD in desalination for a high recovery rate, perhaps even for ZLD.
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Affiliation(s)
- Junghyun Kim
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney (UTS), 15 Broadway, NSW 2007, Australia; Department of Civil, Environmental, and Architectural Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Leonard Tijing
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney (UTS), 15 Broadway, NSW 2007, Australia; ARC Research Hub for Nutrients in a Circular Economy, University of Technology Sydney (UTS), 15 Broadway, NSW 2007, Australia
| | - Ho Kyong Shon
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney (UTS), 15 Broadway, NSW 2007, Australia; ARC Research Hub for Nutrients in a Circular Economy, University of Technology Sydney (UTS), 15 Broadway, NSW 2007, Australia.
| | - Seungkwan Hong
- Department of Civil, Environmental, and Architectural Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
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38
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Xiang Y, Lei C, Hu G, Zhou W, Li Y, Huang D. Investigation of 60Co Irradiation on the Volatile Organic Compounds from Finger Citron ( Citri Sarcodactylis Fructus) Using GC-IMS. Foods 2023; 12:3543. [PMID: 37835196 PMCID: PMC10572713 DOI: 10.3390/foods12193543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
In recent years, as the desire for a healthy lifestyle has become more widespread, consumers are gaining an increasing appreciation for safe, high-quality food. Researchers are constantly seeking new ways to protect foods from insect pests and fungi. This study used GC-IMS to analyze the volatile organic compounds and flavor characteristics of Finger Citron in response to different doses of 60Co irradiation. The principal component analysis method was used to explore the overall differences in flavor spectra, and a total of 60 compounds were identified. The fingerprints of volatile organic compounds in the samples showed that the volatile organic compounds with doses of 60Co irradiation in about 0 kGy and 5 kGy are similar, while the 10 kGy samples are quite different. The PCA results showed that the similarity between 0 kGy and 5 kGy was slightly higher, and the difference between 10 kGy and other samples was greater. Therefore, it was determined that 60Co irradiation with a 10 kGy intensity has a significant influence on the content of volatile oils components, while 60Co irradiation with a 5 kGy intensity has little effect. Irradiation technology is demonstrated as a promising method of food sterilization, but the irradiation dose and chemical composition must be taken into consideration.
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Affiliation(s)
- Yun Xiang
- State Key Laboratory of Chinese Medicine Powder and Medicine Innovation in Hunan (Incubation), Science and Technology Innovation Center, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.X.); (C.L.); (G.H.); (W.Z.)
| | - Chang Lei
- State Key Laboratory of Chinese Medicine Powder and Medicine Innovation in Hunan (Incubation), Science and Technology Innovation Center, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.X.); (C.L.); (G.H.); (W.Z.)
| | - Ge Hu
- State Key Laboratory of Chinese Medicine Powder and Medicine Innovation in Hunan (Incubation), Science and Technology Innovation Center, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.X.); (C.L.); (G.H.); (W.Z.)
| | - Wei Zhou
- State Key Laboratory of Chinese Medicine Powder and Medicine Innovation in Hunan (Incubation), Science and Technology Innovation Center, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.X.); (C.L.); (G.H.); (W.Z.)
| | - Ya Li
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Dan Huang
- State Key Laboratory of Chinese Medicine Powder and Medicine Innovation in Hunan (Incubation), Science and Technology Innovation Center, Hunan University of Chinese Medicine, Changsha 410208, China; (Y.X.); (C.L.); (G.H.); (W.Z.)
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39
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Turzo SMBA, Seffernick JT, Lyskov S, Lindert S. Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver. Brief Bioinform 2023; 24:bbad308. [PMID: 37609950 PMCID: PMC10516336 DOI: 10.1093/bib/bbad308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023] Open
Abstract
Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM). Although there are several computational methods for predicting CCSIM based on protein structures, including our previously developed projection approximation using rough circular shapes (PARCS), the process usually requires prior experience with the command-line interface. To overcome this challenge, here we present a web application on the Rosetta Online Server that Includes Everyone (ROSIE) webserver to predict CCSIM from protein structure using projection approximation with PARCS. In this web interface, the user is only required to provide one or more PDB files as input. Results from our case studies suggest that CCSIM predictions (with ROSIE-PARCS) are highly accurate with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help in distinguishing accurate from inaccurate AlphaFold2 protein structure predictions. ROSIE-PARCS is designed with a user-friendly interface, is available publicly and is free to use. The ROSIE-PARCS web interface is supported by all major web browsers and can be accessed via this link (https://rosie.graylab.jhu.edu).
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Affiliation(s)
- S M Bargeen Alam Turzo
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA
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40
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Williamson DL, Nagy G. Coupling Isotopic Shifts with Collision Cross-Section Measurements for Carbohydrate Characterization in High-Resolution Ion Mobility Separations. Anal Chem 2023; 95:13992-14000. [PMID: 37683280 PMCID: PMC10538943 DOI: 10.1021/acs.analchem.3c02619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Herein, we introduce a two-dimensional strategy to better characterize carbohydrate isomers. In a single experiment, we can derive cyclic ion mobility-mass spectrometry (cIMS-MS)-based collision cross-section (CCS) values in conjunction with measuring isotopic shifts through the relative arrival times of light and heavy isotopologues. These isotopic shifts were introduced by permethylating carbohydrates with either light, CH3, or heavy, CD3, labels at every available hydroxyl group to generate a light/heavy pair of isotopologues for every individual species analyzed. We observed that our calculated CCS values, which were exclusively measured for the light isotopologues, were orthogonal to our measured isotopic shifts (i.e., relative arrival time values between heavy and light permethylated isotopologues). Our permethylation-induced isotopic shifts scaled well with increasing molecular weight, up to ∼m/z 1300, expanding the analysis of isotopic shifts to molecules 3-4 times as large as those previously studied. Our presented use of coupling CCS values with the measurement of isotopic shifts in a single cIMS-MS experiment is a proof-of-concept demonstration that our two-dimensional approach can improve the characterization of challenging isomeric carbohydrates. We envision that our presented 2D approach will have broad utility for varying molecular classes as well as being amenable to many forms of derivatization.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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41
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Rolland AD, Takata T, Donor MT, Lampi KJ, Prell JS. Eye lens β-crystallins are predicted by native ion mobility-mass spectrometry and computations to form compact higher-ordered heterooligomers. Structure 2023; 31:1052-1064.e3. [PMID: 37453416 PMCID: PMC10528727 DOI: 10.1016/j.str.2023.06.013] [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: 10/24/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Eye lens α- and β-/γ-crystallin proteins are not replaced after fiber cell denucleation and maintain lens transparency and refractive properties. The exceptionally high (∼400-500 mg/mL) concentration of crystallins in mature lens tissue and multiple other factors impede precise characterization of β-crystallin interactions, oligomer composition, size, and topology. Native ion mobility-mass spectrometry is used here to probe β-crystallin association and provide insight into homo- and heterooligomerization kinetics for these proteins. These experiments include separation and characterization of higher-order β-crystallin oligomers and illustrate the unique advantages of native IM-MS. Recombinantly expressed βB1, βB2, and βA3 isoforms are found to have different homodimerization propensities, and only βA3 forms larger homooligomers. Heterodimerization of βB2 with βA3 occurs ∼3 times as fast as that of βB1 with βA3, and βB1 and βB2 heterodimerize less readily. Ion mobility experiments, molecular dynamics simulations, and PISA analysis together reveal that observed oligomers are consistent with predominantly compact, ring-like topologies.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA
| | - Takumi Takata
- Kyoto University, Research Reactor Institute 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Micah T Donor
- Department of Biological & Molecular Sciences, George Fox University, 414 N Meridian St, Newberg, OR 97132, USA
| | - Kirsten J Lampi
- Integrative Biosciences, School of Dentistry, 3181 SW Sam Jackson Park Road, Oregon Health & Science University, Portland, OR 97239-3098, USA.
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA; Materials Science Institute, 1252 University of Oregon, Eugene, OR 97403-1252, USA.
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42
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Lübbert C, Supper M, Kaspereit M, Walter J, Peukert W. Single-Molecule Pycnometry and Shape Analysis of Ions in the Gas Phase. Anal Chem 2023; 95:13010-13017. [PMID: 37602575 DOI: 10.1021/acs.analchem.3c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The analysis of ions and clusters by mobility-classified mass spectrometry provides information on the mobility of analytes in the drift gas and the analyte mass. Mass equivalent and mobility equivalent diameters of globular analytes, such as ions, poly(ethylene glycol) (PEG), and ionic liquid nanodroplets, can be correlated with good accuracy by the Stokes-Millikan mobility model. A prerequisite to such an analysis is, however, the assumption of a globular analyte shape, which then allows determination of material density for globular ions. We show that the analyte density can be evaluated with high precision, independent of any assumptions on the analyte shape, by careful analysis of analyte-PEG-cluster ions following the concept of classical pycnometry. In particular, the analyte is entrapped in a globular PEG-analyte droplet. Based on the now independently derived mobility diameter and volume equivalent diameter, it is possible to attribute two parameters, size and shape, to the analyte molecule. We demonstrate the approach for lysozyme, cyano-cobalamin (vitamin B12), and glucose, which cover two orders of magnitude in analyte mass (180···14 300 Da). The derived densities for these analytes are highly accurate, i.e., they deviate less than 1% from literature values. Our method can be applied to newly synthesized molecules, supramolecular assemblies, isolated biomolecules, and molecular clusters, where only minor amounts of materials are available. The obtained shape parameters of lysozyme and cyano-cobalamin agree well with the expected molecular shapes. Data evaluation relies only on locations of the species in the mass-mobility plane and is in principle independent of any mobility theory. Our approach is thus robust with respect to experimental uncertainties and produces identical results irrespective of the type of mobility classification and drift gas.
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Affiliation(s)
- Christian Lübbert
- Institute of Particle Technology, Friedrich Alexander University Erlangen Nuremberg, Interdisciplinary Center for Functional Particle Systems (FPS), Haberstr. 9a, 91058 Erlangen, Germany
| | - Malvina Supper
- Institute of Separation Science and Technology, Friedrich Alexander University Erlangen Nuremberg, Egerlandstraße 3, 91058 Erlangen, Germany
| | - Malte Kaspereit
- Institute of Separation Science and Technology, Friedrich Alexander University Erlangen Nuremberg, Egerlandstraße 3, 91058 Erlangen, Germany
| | - Johannes Walter
- Institute of Particle Technology, Friedrich Alexander University Erlangen Nuremberg, Interdisciplinary Center for Functional Particle Systems (FPS), Haberstr. 9a, 91058 Erlangen, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology, Friedrich Alexander University Erlangen Nuremberg, Interdisciplinary Center for Functional Particle Systems (FPS), Haberstr. 9a, 91058 Erlangen, Germany
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43
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Teschner D, Gomez-Zepeda D, Declercq A, Łącki MK, Avci S, Bob K, Distler U, Michna T, Martens L, Tenzer S, Hildebrandt A. Ionmob: a Python package for prediction of peptide collisional cross-section values. Bioinformatics 2023; 39:btad486. [PMID: 37540201 PMCID: PMC10521631 DOI: 10.1093/bioinformatics/btad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/30/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
MOTIVATION Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived mobility of an ion to its collisional cross-section (CCS), a highly reproducible physicochemical property dependent on the ion's mass, charge and conformation in the gas phase. Thus, known peptide ion mobilities can be used to tailor acquisition methods or to refine database search results. The large space of potential peptide sequences, driven also by posttranslational modifications of amino acids, motivates an in silico predictor for peptide CCS. Recent studies explored the general performance of varying machine-learning techniques, however, the workflow engineering part was of secondary importance. For the sake of applicability, such a tool should be generic, data driven, and offer the possibility to be easily adapted to individual workflows for experimental design and data processing. RESULTS We created ionmob, a Python-based framework for data preparation, training, and prediction of collisional cross-section values of peptides. It is easily customizable and includes a set of pretrained, ready-to-use models and preprocessing routines for training and inference. Using a set of ≈21 000 unique phosphorylated peptides and ≈17 000 MHC ligand sequences and charge state pairs, we expand upon the space of peptides that can be integrated into CCS prediction. Lastly, we investigate the applicability of in silico predicted CCS to increase confidence in identified peptides by applying methods of re-scoring and demonstrate that predicted CCS values complement existing predictors for that task. AVAILABILITY AND IMPLEMENTATION The Python package is available at github: https://github.com/theGreatHerrLebert/ionmob.
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Affiliation(s)
- David Teschner
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - David Gomez-Zepeda
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Mateusz K Łącki
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Seymen Avci
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Konstantin Bob
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
- Immunoproteomics Unit, Helmholtz-Institute for Translational Oncology (HI-TRON), 55131 Mainz, Germany
| | - Andreas Hildebrandt
- Institute of Computer Science, Johannes Gutenberg University, 55128 Mainz, Germany
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44
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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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45
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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46
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Das S, Dinpazhoh L, Tanemura KA, Merz KM. Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input. J Chem Inf Model 2023; 63:4995-5000. [PMID: 37548575 DOI: 10.1021/acs.jcim.3c00890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
We implemented an ab initio CCS prediction workflow which incrementally refines generated structures using molecular mechanics, a deep learning potential, conformational clustering, and quantum mechanics (QM). Automating intermediate steps for a high performance computing (HPC) environment allows users to input the SMILES structure of small organic molecules and obtain a Boltzmann averaged collisional cross section (CCS) value as output. The CCS of a molecular species is a metric measured by ion mobility spectrometry (IMS) which can improve annotation of untargeted metabolomics experiments. We report only a minor drop in accuracy when we expedite the CCS calculation by replacing the QM geometry refinement step with a single-point energy calculation. Even though the workflow involves stochastic steps (i.e., conformation generation and clustering), the final CCS value was highly reproducible for multiple iterations on L-carnosine. Finally, we illustrate that the gas phase ensembles modeled for the workflow are intermediate files which can be used for the prediction of other properties such as aqueous phase nuclear magnetic resonance chemical shift prediction. The software is available at the following link: https://github.com/DasSusanta/snakemake_ccs.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Laleh Dinpazhoh
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kiyoto Aramis Tanemura
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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Santos PHC, Moura PC, Vassilenko V. Suitability of Short- and Long-Term Storage of Volatile Organic Compounds Samples in Syringe-Based Containers: A Comparison Study. Metabolites 2023; 13:903. [PMID: 37623847 PMCID: PMC10456467 DOI: 10.3390/metabo13080903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
The employment of advanced analytical techniques and instrumentation enables the tracing of volatile organic compounds (VOCs) in vestigial concentrations (ppbv-pptv range) for several emerging applications, such as the research of disease biomarkers in exhaled air, the detection of metabolites in several biological processes, and the detection of pollutants for air quality control. In this scope, the storage of gaseous samples is crucial for preserving the integrity and stability of the collected set of analytes. This study aims to assess the suitability of three commercially available syringes as air containers (AC) that are commonly used for the collection, storage, isolation, and transportation of samples: glass syringes with glass plungers (AC1), and two plastic syringes, one with plastic plungers (AC2), and one with rubbered plungers (AC3). For this purpose, 99 air samples with different times of storage (from 10 min to 24 h) were analyzed using a Gas Chromatography-Ion Mobility Spectrometry device and the degradation of the samples was properly assessed by comparing the changes in the VOCs' emission profiles. The quality of the method was assured by via the measurement of the blank's spectra before each experimental run, as well as by the consecutive measurement of the three replicates for each sample. A statistical analysis of the changes in the VOCs' emission patterns was performed using principal component analysis (PCA). The results, with a total explained variance of 93.61%, indicate that AC3 is the most suitable option for the long-term storage of air samples. Thus, AC3 containers demonstrated a higher capacity to preserve the stability and integrity of the analytes compared to AC1 and AC2. The findings of the short-term effects analysis, up to 1 h, confirm the suitability of all analyzed syringe-based containers for sample-transferring purposes in onsite analysis.
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Affiliation(s)
- Paulo Henrique Costa Santos
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-NOVA, 2829-516 Caparica, Portugal;
- NMT, S. A., Edifício Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Pedro Catalão Moura
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-NOVA, 2829-516 Caparica, Portugal;
| | - Valentina Vassilenko
- Laboratory for Instrumentation, Biomedical Engineering and Radiation Physics (LIBPhys-UNL), Department of Physics, NOVA School of Science and Technology, NOVA University of Lisbon, Campus FCT-NOVA, 2829-516 Caparica, Portugal;
- NMT, S. A., Edifício Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
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Peris-Díaz MD, Wu S, Mosna K, Liggett E, Barkhanskiy A, Orzeł A, Barran P, Krężel A. Structural Characterization of Cu(I)/Zn(II)-metallothionein-3 by Ion Mobility Mass Spectrometry and Top-Down Mass Spectrometry. Anal Chem 2023; 95:10966-10974. [PMID: 37440218 PMCID: PMC10372872 DOI: 10.1021/acs.analchem.3c00989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/29/2023] [Indexed: 07/14/2023]
Abstract
Mammalian zinc metallothionein-3 (Zn7MT3) plays an important role in protecting against copper toxicity by scavenging free Cu(II) ions or removing Cu(II) bound to β-amyloid and α-synuclein. While previous studies reported that Zn7MT3 reacts with Cu(II) ions to form Cu(I)4Zn(II)4MT3ox containing two disulfides (ox), the precise localization of the metal ions and disulfides remained unclear. Here, we undertook comprehensive structural characterization of the metal-protein complexes formed by the reaction between Zn7MT3 and Cu(II) ions using native ion mobility mass spectrometry (IM-MS). The complex formation mechanism was found to involve the disassembly of Zn3S9 and Zn4S11 clusters from Zn7MT3 and reassembly into Cu(I)xZn(II)yMT3ox complexes rather than simply Zn(II)-to-Cu(I) exchange. At neutral pH, the β-domain was shown to be capable of binding up to six Cu(I) ions to form Cu(I)6Zn(II)4MT3ox, although the most predominant species was the Cu(I)4Zn(II)4MT3ox complex. Under acidic conditions, four Zn(II) ions dissociate, but the Cu(I)4-thiolate cluster remains stable, highlighting the MT3 role as a Cu(II) scavenger even at lower than the cytosolic pH. IM-derived collision cross sections (CCS) reveal that Cu(I)-to-Zn(II) swap in Zn7MT3 with concomitant disulfide formation induces structural compaction and a decrease in conformational heterogeneity. Collision-induced unfolding (CIU) experiments estimated that the native-like folded Cu(I)4Zn(II)4MT3ox conformation is more stable than Zn7MT3. Native top-down MS demonstrated that the Cu(I) ions are exclusively bound to the β-domain in the Cu(I)4Zn(II)4MT3ox complex as well as the two disulfides, serving as a steric constraint for the Cu(I)4-thiolate cluster. In conclusion, this study enhances our comprehension of the structure, stability, and dynamics of Cu(I)xZn(II)yMT3ox complexes.
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Affiliation(s)
- Manuel David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Sylwia Wu
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Karolina Mosna
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Ellen Liggett
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Alexey Barkhanskiy
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Alicja Orzeł
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Perdita Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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49
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Duez Q, Hoyas S, Josse T, Cornil J, Gerbaux P, De Winter J. Gas-phase structure of polymer ions: Tying together theoretical approaches and ion mobility spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:1129-1151. [PMID: 34747528 DOI: 10.1002/mas.21745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 06/07/2023]
Abstract
An increasing number of studies take advantage of ion mobility spectrometry (IMS) coupled to mass spectrometry (IMS-MS) to investigate the spatial structure of gaseous ions. Synthetic polymers occupy a unique place in the field of IMS-MS. Indeed, due to their intrinsic dispersity, they offer a broad range of homologous ions with different lengths. To help rationalize experimental data, various theoretical approaches have been described. First, the study of trend lines is proposed to derive physicochemical and structural parameters. However, the evaluation of data fitting reflects the overall behavior of the ions without reflecting specific information on their conformation. Atomistic simulations constitute another approach that provide accurate information about the ion shape. The overall scope of this review is dedicated to the synergy between IMS-MS and theoretical approaches, including computational chemistry, demonstrating the essential role they play to fully understand/interpret IMS-MS data.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
| | - Sébastien Hoyas
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
| | | | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, Mons, Belgium
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50
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Haack A, Ieritano C, Hopkins WS. MobCal-MPI 2.0: an accurate and parallelized package for calculating field-dependent collision cross sections and ion mobilities. Analyst 2023. [PMID: 37376881 DOI: 10.1039/d3an00545c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Ion mobility spectrometry (IMS), which can be employed as either a stand-alone instrument or coupled to mass spectrometry, has become an important tool for analytical chemistry. Because of the direct relation between an ion's mobility and its structure, which is intrinsically related to its collision cross section (CCS), IMS techniques can be used in tandem with computational tools to elucidate ion geometric structure. Here, we present MobCal-MPI 2.0, a software package that demonstrates excellent accuracy (RMSE 2.16%) and efficiency in calculating low-field CCSs via the trajectory method (≤30 minutes on 8 cores for ions with ≤70 atoms). MobCal-MPI 2.0 expands on its predecessor by enabling the calculation of high-field mobilities through the implementation of the 2nd order approximation to two-temperature theory (2TT). By further introducing an empirical correction to account for deviations between 2TT and experiment, MobCal-MPI 2.0 can compute accurate high-field mobilities that exhibit a mean deviation of <4% from experimentally measured values. Moreover, the velocities used to sample ion-neutral collisions were updated from a weighted to a linear grid, enabling the near-instantaneous evaluation of mobility/CCS at any effective temperature from a single set of N2 scattering trajectories. Several enhancements made to the code are also discussed, including updates to the statistical analysis of collision event sampling and benchmarking of overall performance.
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Affiliation(s)
- Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
| | - Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
- Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
- Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, 999077, Hong Kong
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