1
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Prell JS. Modeling collisional kinetic energy damping, heating, and cooling of ions in mass spectrometers: a tutorial perspective. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 504:117290. [PMID: 39072228 PMCID: PMC11271708 DOI: 10.1016/j.ijms.2024.117290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Many powerful methods in mass spectrometry rely on activation of ions by high-energy collisions with gas particles. For example, multiple Collision Induced Dissociation (CID) has been used for many years to determine structural information for ions ranging from small organics to large, native-like protein complexes. More recently, Collision Induced Unfolding (CIU) has proved to be a very powerful method for understanding high-order protein structure and detecting differences between similar proteins. Quantifying the thermochemistry underlying dissociation/unfolding in these experiments can be quite challenging without reliable models of ion heating and cooling. Established physical models of CID are valuable in predicting ion heating but do not explicitly include mechanisms for cooling, which may play a large part in CID/CIU in modern instruments. Ab initio and Molecular Dynamics methods are extremely computationally expensive for modeling CID/CIU of large analytes such as biomolecular ions. In this tutorial perspective, limiting behaviors of ion kinetic energy damping, heating, and cooling set by "extreme" cases are explored, and an Improved Impulsive Collision Theory and associated software ("Ion Simulations of the Physics of Activation", IonSPA) are introduced that can model all of these for partially inelastic collisions. Finally, examples of modeled collisional activation of native-like protein ions under realistic experimental conditions are discussed, with an outlook toward the use of IonSPA in accessing the thermochemical information hidden in CID breakdown curves and CIU fingerprints.
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Affiliation(s)
- James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, OR, USA, 97403-1252
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2
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Benoit F, Wang X, Dai J, Geue N, England RM, Bristow AWT, Barran PE. Exploring the Conformational Landscape of Poly(l-lysine) Dendrimers Using Ion Mobility Mass Spectrometry. Anal Chem 2024; 96:9390-9398. [PMID: 38812282 PMCID: PMC11170554 DOI: 10.1021/acs.analchem.4c00099] [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: 01/05/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
Ion mobility mass spectrometry (IM-MS) measures the mass, size, and shape of ions in the same experiment, and structural information is provided via collision cross-section (CCS) values. The majority of commercially available IM-MS instrumentation relies on the use of CCS calibrants, and here, we present data from a family of poly(l-lysine) dendrimers and explore their suitability for this purpose. In order to test these compounds, we employed three different IM-MS platforms (Agilent 6560 IM-QToF, Waters Synapt G2, and a home-built variable temperature drift tube IM-MS) and used them to investigate six different generations of dendrimers in two buffer gases (helium and nitrogen). Each molecule gives a highly discrete CCS distribution suggestive of single conformers for each m/z value. The DTCCSN2 values of this series of molecules (molecular weight: 330-16,214 Da) range from 182 to 2941 Å2, which spans the CCS range that would be found by many synthetic molecules including supramolecular compounds and many biopolymers. The CCS values for each charge state were highly reproducible in day-to-day analysis on each instrument, although we found small variations in the absolute CCS values between instruments. The rigidity of each dendrimer was probed using collisionally activated and high-temperature IM-MS experiments, where no evidence for a significant CCS change ensued. Taken together, this data indicates that these polymers are candidates for CCS calibration and could also help to reconcile differences found in CCS measurements on different instrument geometries.
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Affiliation(s)
- Florian Benoit
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Xudong Wang
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Junxiao Dai
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Richard M. England
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Anthony W. T. Bristow
- Chemical
Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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3
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Kumar M, Attygalle AB. Manipulating Non-Dissociative Transformations of Gaseous Ion Ensembles Prior to Ion-Mobility Separation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1197-1207. [PMID: 38718179 DOI: 10.1021/jasms.4c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Molecules with multiple sites capable of accepting protons form ensembles of protomers. The manifested protomer ratios in such ensembles are influenced by many experimental conditions. In a Synapt G2 ion mobility (IM)-enabled mass spectrometry system, there are several physical locations where ion population changes can be manifested. Using APCI-generated protomers of aminonaphthalenes, we investigated its intramolecular proton transfers from the N-protomer to the C-protomer. This lossless transformation of the N-protomer to the thermodynamically favored C-protomer can take place in the ion source itself. Initially, we learned that the cone gas slows down the transformation to the C-protomer. Gaseous ions are then accelerated in the first vacuum region, where ions undergo collisional activation (heating), which facilitates the transformation to the C-protomer. Afterward, the ions are mass selected and transferred to the pre-IM (Trap)-collision cell, where ions can also be transformed to the thermodynamically favored protomers. Trap accumulated ions are then released to the IM separator via a helium-filled entry cell. The role of helium is to minimize ion activation and scattering taking place upon entry to the high-pressure T-Wave IM separator (TWIMS). The helium cell is known to increase the IM peak resolution. However, we found that significant changes occur depending on the presence or absence of helium. Without helium, source-generated protomers rapidly changed to a predominantly thermodynamically favorable ensemble protomers. Apparently, the introduction of helium into the precell induced a dramatic decrease in collisional "heating" effect, which effectively slowed down the conversion rate of the amino-protomer into the more favorable ring-protomer. The final message is that mobilograms should not be considered as direct real-time, or intrinsic, representations of the protomer ratios in the ion source.
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Affiliation(s)
- Meenu Kumar
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Athula B Attygalle
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
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4
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Kurilung A, Limjiasahapong S, Kaewnarin K, Wisanpitayakorn P, Jariyasopit N, Wanichthanarak K, Sartyoungkul S, Wong SCC, Sathirapongsasuti N, Kitiyakara C, Sirivatanauksorn Y, Khoomrung S. Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples. J Pharm Anal 2024; 14:100921. [PMID: 38799238 PMCID: PMC11127212 DOI: 10.1016/j.jpha.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/17/2023] [Accepted: 12/13/2023] [Indexed: 05/29/2024] Open
Abstract
The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method using ultrahigh-performance liquid chromatography (UPLC) coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples. The experimental CCS values, along with mass spectral properties, were reported for the 174 metabolites. The experimental data included the mass-to-charge ratio (m/z), retention time (RT), tandem MS (MS/MS) spectra, and CCS values. Among the studied metabolites, 263 traveling wave ion mobility spectrometry (TWIMS)-derived CCS values (TWCCSN2) were reported for the first time, and more than 70% of these were CCS values of VLMs. The TWCCSN2 values were highly repeatable, with inter-day variations of <1% relative standard deviation (RSD). The developed method revealed excellent TWCCSN2 accuracy with a CCS difference (ΔCCS) within ±2% of the reported drift tube IMS (DTIMS) and TWIMS CCS values. The complexity of the urine matrix did not affect the precision of the method, as evidenced by ΔCCS within ±1.92%. According to the Metabolomics Standards Initiative, 55 urinary metabolites were identified with a confidence level of 1. Among these 55 metabolites, 53 (96%) were VLMs. The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values, which clearly increased metabolite identification confidence.
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Affiliation(s)
- Alongkorn Kurilung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Suphitcha Limjiasahapong
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Khwanta Kaewnarin
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- SingHealth Duke-NUS Institute of Biodiversity Medicine, National Cancer Centre Singapore, 168583, Singapore
| | - Pattipong Wisanpitayakorn
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Narumol Jariyasopit
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Kwanjeera Wanichthanarak
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sitanan Sartyoungkul
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | | | - Nuankanya Sathirapongsasuti
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, 10540, Thailand
| | - Chagriya Kitiyakara
- Department of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellent in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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5
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Kinlein Z, Clowers BH. Altering Conformational States of Dynamic Ion Populations using Traveling Wave Structures for Lossless Ion Manipulations. Anal Chem 2024; 96:6450-6458. [PMID: 38603648 DOI: 10.1021/acs.analchem.4c00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
With its capacity to store and translate ions across considerable distances and times, traveling wave structures for lossless ion manipulations (TW-SLIM) provide the foundation to expand the scope of ion mobility spectrometry (IMS) experiments. While promising, the dynamic electric fields and consequential ion-neutral collisions used to realize extensive degrees of separation have a considerable impact on the empirical results and the fundamental interpretation of observed arrival time distributions. Using a custom-designed set of TW-SLIM boards (∼9 m) coupled with a time-of-flight mass spectrometer (SLIM-ToF), we detail the capacity to systematically alter the gas-phase distribution of select peptide conformers. In addition to discussing the role charge-transfer may play in TW-SLIM experiments that occur at extended time scales, the ability of the SLIM-ToF to perform tandem IMS was leveraged to confirm that both the compact and elongated conformers of bradykinin2+ undergo interconversion within the SLIM. Storage experiments in which ions are confined within SLIM using static potential wells suggest that factors aside from TW-induced ion motion contribute to interconversion. Further investigation into this matter suggests that the use of radio frequency (RF) fields to confine ions within SLIM may play a role in ion heating. Aside from interconversion, storage experiments also provide insight into charge transfer behavior over the course of extended periods. The results of the presented experiments suggest that considerations should be taken when analyzing labile species and inform strategies for the TW-SLIM design and method development.
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Affiliation(s)
- Zackary Kinlein
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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6
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Stroganova I, Willenberg H, Tente T, Depraz Depland A, Bakels S, Rijs AM. Exploring the Aggregation Propensity of PHF6 Peptide Segments of the Tau Protein Using Ion Mobility Mass Spectrometry Techniques. Anal Chem 2024; 96:5115-5124. [PMID: 38517679 PMCID: PMC10993201 DOI: 10.1021/acs.analchem.3c04974] [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: 11/03/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024]
Abstract
Peptide and protein aggregation involves the formation of oligomeric species, but the complex interplay between oligomers of different conformations and sizes complicates their structural elucidation. Using ion mobility mass spectrometry (IM-MS), we aim to reveal these early steps of aggregation for the Ac-PHF6-NH2 peptide segment from tau protein, thereby distinguishing between different oligomeric species and gaining an understanding of the aggregation pathway. An important factor that is often neglected, but which can alter the aggregation propensity of peptides, is the terminal capping groups. Here, we demonstrate the use of IM-MS to probe the early stages of aggregate formation of Ac-PHF6-NH2, Ac-PHF6, PHF6-NH2, and uncapped PHF6 peptide segments. The aggregation propensity of the four PHF6 segments is confirmed using thioflavin T fluorescence assays and transmission electron microscopy. A novel approach based on post-IM fragmentation and quadrupole selection on the TIMS-Qq-ToF (trapped ion mobility) spectrometer was developed to enhance oligomer assignment, especially for the higher-order aggregates. This approach pushes the limits of IM identification of isobaric species, whose signatures appear closer to each other with increasing oligomer size, and provides new insights into the interpretation of IM-MS data. In addition, TIMS collision cross section values are compared with traveling wave ion mobility (TWIMS) data to evaluate potential instrumental bias in the trapped ion mobility results. The two IM-MS instrumental platforms are based on different ion mobility principles and have different configurations, thereby providing us with valuable insight into the preservation of weakly bound biomolecular complexes such as peptide aggregates.
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Affiliation(s)
- Iuliia Stroganova
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Hannah Willenberg
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
| | - Thaleia Tente
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
| | - Agathe Depraz Depland
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Sjors Bakels
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Anouk M. Rijs
- Division
of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical
Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The Netherlands
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7
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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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8
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Poltash ML, Srzentić K, Beil E, Gorre E, Damoc E, Mahan AD, Nanda H, Chowdhury P. Elucidating the Mechanism of Multispecific Antibody Aggregation through Subunit Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2654-2661. [PMID: 37922506 DOI: 10.1021/jasms.3c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Multispecific antibody constructs are quickly becoming more common constructs in biopharmaceuticals to improve specificity and efficacy. While the advent of this technology has led to improved therapeutics, its development has challenged the analytical tools through which these therapeutics are characterized. Moreover, new critical quality attributes, such as aggregation, have challenged the approaches to characterization even further. Herein, we describe a novel native subunit analysis using IdeS and IgdE analyzed by native size exclusion chromatography coupled with mass spectrometry to interrogate the mechanism of aggregation in a multispecific antibody. Digestion by IdeS and IdgE allows for the retention and detection of noncovalent interactions thereafter. Aggregation was localized to single-chain fragment variables (scFvs) wherein a domain swapping mechanism between VH1/VL2 and VH2/VL1 occurs.
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Affiliation(s)
- Michael L Poltash
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
| | | | - Eric Beil
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
| | - Elsa Gorre
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
| | - Eugen Damoc
- Thermo Fisher Scientific, 28199 Bremen, Germany
| | - Andrew D Mahan
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
| | - Hirsh Nanda
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
| | - Partha Chowdhury
- Janssen Pharmaceuticals Research and Development, Spring House, Pennsylvania 19477, United States
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9
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Rangel-Angarita V, Mahoney KE, Kwon C, Sarker R, Lucas TM, Malaker SA. False-Positive Glycopeptide Identification via In-FAIMS Fragmentation. JACS AU 2023; 3:2498-2509. [PMID: 37772174 PMCID: PMC10523363 DOI: 10.1021/jacsau.3c00264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/30/2023]
Abstract
High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates glycopeptides in the gas phase prior to mass spectrometry (MS) analysis, thus offering the potential to analyze glycopeptides without prior enrichment. Several studies have demonstrated the ability of FAIMS to enhance glycopeptide detection but have primarily focused on N-glycosylation. Here, we evaluated FAIMS for O-glycoprotein and mucin-domain glycoprotein analysis using samples of varying complexity. We demonstrated that FAIMS was useful in increasingly complex samples as it allowed for the identification of more glycosylated species. However, during our analyses, we observed a phenomenon called "in FAIMS fragmentation" (IFF) akin to in source fragmentation but occurring during FAIMS separation. FAIMS experiments showed a 2- to 5-fold increase in spectral matches from IFF compared with control experiments. These results were also replicated in previously published data, indicating that this is likely a systemic occurrence when using FAIMS. Our study highlights that although there are potential benefits to using FAIMS separation, caution must be exercised in data analysis because of prevalent IFF, which may limit its applicability in the broader field of O-glycoproteomics.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Keira E. Mahoney
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Catherine Kwon
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Raibat Sarker
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
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10
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Moses T, Burgess K. Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics. Front Mol Biosci 2023; 10:1230282. [PMID: 37602325 PMCID: PMC10436490 DOI: 10.3389/fmolb.2023.1230282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15 years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.
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Affiliation(s)
- Tessa Moses
- EdinOmics, RRID:SCR_021838, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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11
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Zercher BP, Hong S, Roush AE, Feng Y, Bush MF. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Anal Chem 2023; 95:9589-9597. [PMID: 37294019 PMCID: PMC10549206 DOI: 10.1021/acs.analchem.3c01222] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Seoyeon Hong
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Addison E. Roush
- 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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12
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Haack A, Schaefer C, Zimmermann S, Hopkins WS. Validation of Field-Dependent Ion-Solvent Cluster Modeling via Direct Measurement of Cluster Size Distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1035-1046. [PMID: 37116175 DOI: 10.1021/jasms.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ion mobility spectrometry is widely used in analytical chemistry, either as a stand-alone technique or coupled to mass spectrometry. Ions in the gas phase tend to form loosely bound clusters with surrounding solvent vapors, artificially increasing the collisional cross section and the mass of the ion. This, in turn, affects ion mobility and influences separation. Further, ion-solvent clusters play an important role in most ionization mechanisms occurring in the gas phase. Consequently, a deeper understanding of ion-solvent cluster association and dissociation processes is desirable to guide experimental design and interpretation. A few computational models exist, which aim to describe the amount of clustering as a function of the reduced electric field strength, bath gas pressure and temperature, and the chemical species probed. It is especially challenging to model ion mobility under high reduced electrical field strengths due to the nonthermal conditions created by the field. In this work, we aim to validate a recently proposed first-principles model by comparing its predictions with direct measurements of cluster size distributions over a range of 20-120 Td as observed using a High Kinetic Energy Ion Mobility Spectrometer coupled to a mass spectrometer (HiKE-IMS-MS). By studying H+(H2O)n, [MeOH + H + n(H2O)]+, [ACE + H + n(H2O)]+, and [PhNH2 + H + n(H2O)]+ as test systems, we find very good agreement between model and experiment, supporting the validity of the computational workflow. Further, the detailed information gained from the modeling yields important insights into the cluster dynamics within the HiKE-IMS, allowing for better interpretation of the measured ion mobility spectra.
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Affiliation(s)
- Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, Ontario N2L 3G1, Canada
| | - Christoph Schaefer
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - Stefan Zimmermann
- Department of Sensors and Measurement Technology, Institute of Electrical Engineering and Measurement Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, Ontario 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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13
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Gandhi VD, Lee J, Hua L, Latif M, Hogan CJ, Larriba-Andaluz C. Investigation of Zero-/High-Field Ion Mobility Orthogonal Separation Using a Hyphenated DMA-FAIMS System and Validation of the Two-Temperature Theory at Arbitrary Field for Tetraalkylammonium Salts in Nitrogen. Anal Chem 2023; 95:7941-7949. [PMID: 37172072 DOI: 10.1021/acs.analchem.3c00509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Toward greater separation techniques for ions, a differential mobility analyzer (DMA) has been coupled with field asymmetric waveform ion mobility spectrometry (FAIMS) to take advantage of two mobility-related but different methods of separation. The filtering effect of the DMA allows ions to be selected individually based on low-field mobility and studied in FAIMS at variable electric field, yielding mobility separations in two dimensions. Because spectra fully describe ion mobility at variable field strength, results are then compared with a two-temperature theory-predicted mobility up to the fourth-order approximation. The comparison yields excellent results up to at least 100 Td, beyond which the theory deviates from experiments. This is attributed to two effects, the enlargement of the structure due to ion heating and the inelasticity of the collisions with the nitrogen bath gas. The corrected mobility can then be used to predict the dispersion plot through a newly developed implicit equation that circumvents the possible issues related to the more elaborate Buryakov equation. Our results simultaneously show that the DMA-FAIMS coupling yields complete information on ion mobility versus the field-strength to gas-density ratio and works toward predicting such spectra from ion structures and gas properties.
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Affiliation(s)
- Viraj D Gandhi
- Department of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Jihyeon Lee
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Leyan Hua
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Mohsen Latif
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlos Larriba-Andaluz
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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14
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Cain RL, Webb IK. Online protein unfolding characterized by ion mobility electron capture dissociation mass spectrometry: cytochrome C from neutral and acidic solutions. Anal Bioanal Chem 2023; 415:749-758. [PMID: 36622393 DOI: 10.1007/s00216-022-04501-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) experiments, including ion mobility spectrometry mass spectrometry (ESI-IMS-MS) and electron capture dissociation (ECD) of proteins ionized from aqueous solutions, have been used for the study of solution-like structures of intact proteins. By mixing aqueous proteins with denaturants online before ESI, the amount of protein unfolding can be precisely controlled and rapidly analyzed, permitting the characterization of protein folding intermediates in protein folding pathways. Herein, we mixed various pH solutions online with aqueous cytochrome C for unfolding and characterizing its unfolding intermediates with ESI-MS charge state distribution measurements, IMS, and ECD. The presence of folding intermediates and unfolded cytochrome c structures were detected from changes in charge states, arrival time distributions (ATDs), and ECD. We also compared structures from nondenaturing and denaturing solution mixtures measured under "gentle" (i.e., low energy) ion transmission conditions with structures measured under "harsh" (i.e., higher energy) transmission. This work confirms that when using "gentle" instrument conditions, the gas-phase cytochrome c ions reflect attributes of the various solution-phase structures. However, "harsh" conditions that maximize ion transmission produce extended structures that no longer correlate with changes in solution structure.
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Affiliation(s)
- Rebecca L Cain
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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15
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Naylor CN, Schaefer C, Kirk AT, Zimmermann S. The origin of isomerization of aniline revealed by high kinetic energy ion mobility spectrometry (HiKE-IMS). Phys Chem Chem Phys 2023; 25:1139-1152. [PMID: 36515135 DOI: 10.1039/d2cp01994a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although aniline is a relatively simple small molecule, the origin of its two peaks observed in ion mobility spectrometry (IMS) has remained under debate for at least 30 years. First hypothesized as a difference in protonation site (amine vs. benzene ring), each ion mobility peak differs by one Dalton when coupled with mass spectrometry where the faster mobility peak is the molecular ion peak, and the slower mobility peak is protonated. To complicate the deconvolution of structures, some previous literature shows the peaks as unresolved and thus proposes these species exist in equilibrium. In this work, we show that when measured with high kinetic energy ion mobility spectrometry (HiKE-IMS), the two peaks observed in spectra of both aniline and all n-fluoroanilines are fully separated (chromatographic resolution from 2-7, Rp > 110) and therefore not in equilibrium. The HiKE-IMS is capable of changing ionization conditions independently of drift region conditions, and our results agree with previous literature showing that ionization source settings (including possible fragmentation at this stage) are the only influence determining the speciation of the two aniline peaks. Finally, when the drift and reactant gas are changed to nitrogen, a third peak appears at high E/N for 2-fluoroaniline and 4-fluoroaniline for the first time in reported literature. As observed by HiKE-IMS-MS, the new third peak is also protonated showing that the para-protonated aniline and resulting fragment ion, molecular ion aniline, can be fully separated in the mobility domain for the first time. The appearance of the third peak is only possible due to the increased separation of the other two peaks within the HiKE-IMS.
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Affiliation(s)
- Cameron N Naylor
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Christoph Schaefer
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Ansgar T Kirk
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Stefan Zimmermann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
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16
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Geue N, Bennett TS, Arama AAM, Ramakers LAI, Whitehead GFS, Timco GA, Armentrout PB, McInnes EJL, Burton NA, Winpenny REP, Barran PE. Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes. J Am Chem Soc 2022; 144:22528-22539. [PMID: 36459680 PMCID: PMC9756338 DOI: 10.1021/jacs.2c07522] [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: 07/30/2022] [Indexed: 12/04/2022]
Abstract
Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH2RR'][Cr7MF8(O2CtBu)16] with M = MnII, FeII, CoII, NiII, CuII, ZnII, CdII. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH2RR']+. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.
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Affiliation(s)
- Niklas Geue
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
| | - Tom S. Bennett
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | | | - Lennart A. I. Ramakers
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
| | - George F. S. Whitehead
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Grigore A. Timco
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, Salt Lake City, Utah84112, United States
| | - Eric J. L. McInnes
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Neil A. Burton
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Richard E. P. Winpenny
- Department
of Chemistry, The University of Manchester, Oxford Road, ManchesterM13 9PL, U.K.
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University
of Manchester, 131 Princess Street, ManchesterM1 7DN, U.K.
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17
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Heravi T, Arslanian AJ, Johnson SD, Dearden DV. Ion Mobility and Fourier Transform Ion Cyclotron Resonance Collision Cross Section Techniques Yield Long-Range and Hard-Sphere Results, Respectively. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1644-1652. [PMID: 35960880 DOI: 10.1021/jasms.2c00112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We determined collision cross section (CCS) values for singly and doubly charged cucurbit[n]uril (n = 5-7), decamethylcucurbit[5]uril, and cyclohexanocucurbit[5]uril complexes of alkali metal cations (Li+-Cs+). These hosts are relatively rigid. CCS values calculated using the projection approximation (PA) for computationally modeled structures of a given host are nearly identical for +1 and +2 complexes, with weak metal ion dependence, whereas trajectory method (TM) calculations of CCS for the same structures consistently yield values 7-10% larger for the +2 complexes than for the corresponding +1 complexes and little metal ion dependence. Experimentally, we measured relative CCS values in SF6 for pairs of +1 and +2 complexes of the cucurbituril hosts using the cross-sectional areas by Fourier transform ion cyclotron resonance ("CRAFTI") method. At center-of-mass collision energies <∼30 eV, CRAFTI CCS values are sensitive to the relative binding energies in the +1 and +2 complexes, but at collision energies >∼40 eV (sufficient that ion decoherence occurs on essentially every collision) that dependence is not evident. Consistent with the PA calculations, these experiments found that the +2 complex ions have CCS values ranging between 94 and 105% of those of their +1 counterparts (increasing with metal ion size). In contrast, but consistent with the TM CCS calculations, ion mobility measurements of the same complexes at close to thermal energies in much less polarizable N2 find the CCS of +2 complexes to be in all cases 9-12% larger than those of the corresponding +1 complexes, with little metal ion dependence.
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Affiliation(s)
- Tina Heravi
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Andrew J Arslanian
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - Spencer D Johnson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
| | - David V Dearden
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-1030, United States
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18
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Detecting the Subtle Photo-Responsive Conformational Bistability of Monomeric Azobenzene Functionalized Keggin Polyoxometalates by Using Ion-Mobility Mass Spectrometry. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123927. [PMID: 35745050 PMCID: PMC9228792 DOI: 10.3390/molecules27123927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/04/2022]
Abstract
Accurately characterizing the conformational variation of novel molecular assemblies is important but often ignored due to limited characterization methods. Herein, we reported the use of ion-mobility mass spectrometry (IMS/MS) to investigate the conformational changes of four azobenzene covalently functionalized Keggin hybrids (azo-Keggins, compounds 1–4). The as-prepared azo-Keggins showed the general molecular formula of [C16H36N]4[SiW11O40(Si(CH2)3NH–CO(CH2)nO–C6H4N=NC6H4–R)2] (R = H, n = 0 (1); R = NO2, n = 0 (2); R = H, n = 5 (3); R = H, n = 10 (4)). The resultant azo-Keggins maintained stable monomeric states in the gas phase with intact molecular structures. Furthermore, the subtle photo-responsive trans-cis conformational variations of azo-Keggins were clearly revealed by the molecular shape-related collision cross-section value difference ranging from 2.44 Å2 to 6.91 Å2. The longer the alkyl chains linkers were, the larger the conformational variation was. Moreover, for compounds 1 and 2, higher stability in trans-conformation can be observed, while for compounds 3 and 4, bistability can be achieved for both of them.
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19
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Andrzejewski R, Entwistle A, Giles R, Shvartsburg AA. Ion Mobility Spectrometry of Superheated Macromolecules at Electric Fields up to 500 Td. Anal Chem 2021; 93:12049-12058. [PMID: 34423987 DOI: 10.1021/acs.analchem.1c02299] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its inception in 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) has been implemented at or near ambient gas pressure. We recently developed FAIMS at 15-30 Torr with mass spectrometry and utilized it to analyze amino acids, isomeric peptides, and protein conformers. The separations broadly mirrored those at atmospheric pressure, save for larger proteins that (as predicted) exhibited dipole alignment at ambient but not low pressure. Here we reduce the pressure down to 4.7 Torr, allowing normalized electric fields up to 543 Td-double the maximum in prior FAIMS or IMS studies of polyatomic ions. Despite the collisional heating to ∼1000 °C at the waveform peaks, the proteins of size from ubiquitin to albumin survived intact. The dissociation of macromolecules in FAIMS appears governed by the average ion temperature over the waveform cycle, unlike the isomerization controlled by the peak temperature. The global separation trends in this "superhot" regime extend those at moderately low pressures, with distinct conformers and no alignment as theorized. Although the scaling of the compensation voltage with the field fell below cubic at lower fields, the resolving power increased and the resolution of different proteins or charge states substantially improved.
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Affiliation(s)
- Roch Andrzejewski
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Andrew Entwistle
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Roger Giles
- Shimadzu Research Laboratory, Wharfside, Trafford Wharf Road, Manchester M17 1GP, U.K
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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20
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Cheung See Kit M, Shepherd SO, Prell JS, Webb IK. Experimental Determination of Activation Energies for Covalent Bond Formation via Ion/Ion Reactions and Competing Processes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2313-2321. [PMID: 33730481 PMCID: PMC9248411 DOI: 10.1021/jasms.1c00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The combination of ion/ion chemistry with commercially available ion mobility/mass spectrometry systems has allowed rich structural information to be obtained for gaseous protein ions. Recently, the simple modification of such an instrument with an electrospray reagent source has allowed three-dimensional gas-phase interrogation of protein structures through covalent and noncovalent interactions coupled with collision cross section measurements. However, the energetics of these processes have not yet been studied quantitatively. In this work, previously developed Monte Carlo simulations of ion temperatures inside traveling wave ion guides are used to characterize the energetics of the transition state of activated ubiquitin cation/sulfo-benzoyl-HOAt reagent anion long-lived complexes formed via ion/ion reactions. The ΔH‡ and ΔS‡ of major processes observed from collisional activation of long-lived gas-phase ion/ion complexes, namely collision induced unfolding (CIU), covalent bond formation, or neutral loss of the anionic reagent via intramolecular proton transfer, were determined. Covalent bond formation via ion/ion complexes was found to be significantly lower energy compared to unfolding and bond cleavage. The ΔG‡ values of activation of all three processes lie between 55 and 75 kJ/mol, easily accessible with moderate collisional activation. Bond formation is favored over reagent loss at lower activation energies, whereas reagent loss becomes competitive at higher collision energies. Though the ΔG‡ values between CIU of a precursor ion and covalent bond formation of its ion/ion product complex are comparable, our data suggest covalent bond formation does not require extensive isomerization.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
- Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Ian K. Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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21
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Connolly JRFB, Munoz-Muriedas J, Lapthorn C, Higton D, Vissers JPC, Webb A, Beaumont C, Dear GJ. Investigation into Small Molecule Isomeric Glucuronide Metabolite Differentiation Using In Silico and Experimental Collision Cross-Section Values. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1976-1986. [PMID: 34296869 DOI: 10.1021/jasms.0c00427] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying isomeric metabolites remains a challenging and time-consuming process with both sensitivity and unambiguous structural assignment typically only achieved through the combined use of LC-MS and NMR. Ion mobility mass spectrometry (IMMS) has the potential to produce timely and accurate data using a single technique to identify drug metabolites, including isomers, without the requirement for in-depth interpretation (cf. MS/MS data) using an automated computational pipeline by comparison of experimental collision cross-section (CCS) values with predicted CCS values. An ion mobility enabled Q-Tof mass spectrometer was used to determine the CCS values of 28 (14 isomeric pairs of) small molecule glucuronide metabolites, which were then compared to two different in silico models; a quantum mechanics (QM) and a machine learning (ML) approach to test these approaches. The difference between CCS values within isomer pairs was also assessed to evaluate if the difference was large enough for unambiguous structural identification through in silico prediction. A good correlation was found between both the QM- and ML-based models and experimentally determined CCS values. The predicted CCS values were found to be similar between ML and QM in silico methods, with the QM model more accurately describing the difference in CCS values between isomer pairs. Of the 14 isomeric pairs, only one (naringenin glucuronides) gave a sufficient difference in CCS values for the QM model to distinguish between the isomers with some level of confidence, with the ML model unable to confidently distinguish the studied isomer pairs. An evaluation of analyte structures was also undertaken to explore any trends or anomalies within the data set.
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Affiliation(s)
- John R F B Connolly
- RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin D02 YN77, Ireland
| | | | - Cris Lapthorn
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Higton
- Waters Corporation, Stamford Ave, Wilmslow SK9 4AX, United Kingdom
| | | | - Alison Webb
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Claire Beaumont
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gordon J Dear
- GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
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22
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Zimnicka M, Kalenius E, Jurczak J, Danikiewicz W. Ion mobility mass spectrometry - an efficient tool for the analysis of conformational switch of macrocyclic receptors upon anion binding. Analyst 2021; 146:5337-5346. [PMID: 34323262 DOI: 10.1039/d1an00958c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions between anions and synthetic macrocyclic receptors belong to the extensively explored area of research due to the particularly important functions of anions in biological and environmental sciences. Structures of anion-macrocycle complexes are closely related to their function, highlighting the importance of structural analysis of the complexes. Here, we discuss the application of ion mobility mass spectrometry (IM-MS) and theoretical calculations to the structural analysis of tetralactam macrocycles (M) with varying flexibility and structural properties, and their complexes with anions [M + X]-. Collision cross section (CCS) values obtained from both direct drift tube (DT) and indirect using traveling-wave (TW) IM-MS measurements supplemented by theoretical calculations were successfully used to describe the structural properties of various macrocycle-anion complexes, proving the suitability of the IM-MS approach for sensitive, selective, and fast detection of anion complexes and characterization of their structures and conformations.
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Affiliation(s)
- Magdalena Zimnicka
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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23
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Ieritano C, Hopkins WS. "Thermometer" Ions Can Fragment Through an Unexpected Intramolecular Elimination: These Are Not the Fragments You Are Looking For. J Phys Chem Lett 2021; 12:5994-5999. [PMID: 34161734 DOI: 10.1021/acs.jpclett.1c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Benzylpyridinium analogs are effective thermometer ions since monitoring the formation of the benzylium fragment produced from heterolytic cleavage of the C-N bond can be linked to the ion's internal energy. In this study, three para-substituted benzylpyridinium ions containing ethoxy (OEt), isopropoxy (OiPr) and tert-butoxy (OtBu) substitutents were synthesized and evaluated as chemical thermometers. Intriguingly, the product ion spectra of the three benzylpyridinium ions were dominated by m/z 107 instead of the anticipated benzylium species. Deuterium labeling suggested that the m/z 107 fragment resulted from an intramolecular elimination (Ei), which formed via a four-membered transition state (TS). The fragmentation pathway appears to be an anomaly within the mass spectrometry literature, as four-membered pericyclic TSs are usually accompanied by the formation of an exceptionally stable neutral molecule (e.g., CO2). Quantum-chemical calculations confirmed our hypothesis that stabilization of the strained TS is afforded by hyperconjugation (ΔG‡ tert-butoxy < isopropyoxy < ethoxy).
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario 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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24
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Lloyd Williams OH, Rijs NJ. Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry. Front Chem 2021; 9:682743. [PMID: 34169059 PMCID: PMC8217442 DOI: 10.3389/fchem.2021.682743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 01/03/2023] Open
Abstract
Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.
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Affiliation(s)
| | - Nicole J. Rijs
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia
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25
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Eldrid C, Ben-Younis A, Ujma J, Britt H, Cragnolini T, Kalfas S, Cooper-Shepherd D, Tomczyk N, Giles K, Morris M, Akter R, Raleigh D, Thalassinos K. Cyclic Ion Mobility-Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1545-1552. [PMID: 34006100 PMCID: PMC8172447 DOI: 10.1021/jasms.1c00018] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ion mobility coupled to mass spectrometry (IM-MS) is widely used to study protein dynamics and structure in the gas phase. Increasing the energy with which the protein ions are introduced to the IM cell can induce them to unfold, providing information on the comparative energetics of unfolding between different proteoforms. Recently, a high-resolution cyclic IM-mass spectrometer (cIM-MS) was introduced, allowing multiple, consecutive tandem IM experiments (IMn) to be carried out. We describe a tandem IM technique for defining detailed protein unfolding pathways and the dynamics of disordered proteins. The method involves multiple rounds of IM separation and collision activation (CA): IM-CA-IM and CA-IM-CA-IM. Here, we explore its application to studies of a model protein, cytochrome C, and dimeric human islet amyloid polypeptide (hIAPP), a cytotoxic and amyloidogenic peptide involved in type II diabetes. In agreement with prior work using single stage IM-MS, several unfolding events are observed for cytochrome C. IMn-MS experiments also show evidence of interconversion between compact and extended structures. IMn-MS data for hIAPP shows interconversion prior to dissociation, suggesting that the certain conformations have low energy barriers between them and transition between compact and extended forms.
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Affiliation(s)
- Charles Eldrid
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Aisha Ben-Younis
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Jakub Ujma
- Waters
Corporation, Wilmslow SK9 4AX, U.K.
| | - Hannah Britt
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Tristan Cragnolini
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K.
| | - Symeon Kalfas
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | | | | | | | | | - Rehana Akter
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Daniel Raleigh
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Konstantinos Thalassinos
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K.
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26
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Konermann L, Aliyari E, Lee JH. Mobile Protons Limit the Stability of Salt Bridges in the Gas Phase: Implications for the Structures of Electrosprayed Protein Ions. J Phys Chem B 2021; 125:3803-3814. [PMID: 33848419 DOI: 10.1021/acs.jpcb.1c00944] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrosprayed protein ions can retain native-like conformations. The intramolecular contacts that stabilize these compact gas-phase structures remain poorly understood. Recent work has uncovered abundant salt bridges in electrosprayed proteins. Salt bridges are zwitterionic BH+/A- contacts. The low dielectric constant in the vacuum strengthens electrostatic interactions, suggesting that salt bridges could be a key contributor to the retention of compact protein structures. A problem with this assertion is that H+ are mobile, such that H+ transfer can convert salt bridges into neutral B0/HA0 contacts. This possible salt bridge annihilation puts into question the role of zwitterionic motifs in the gas phase, and it calls for a detailed analysis of BH+/A- versus B0/HA0 interactions. Here, we investigate this issue using molecular dynamics (MD) simulations and electrospray experiments. MD data for short model peptides revealed that salt bridges with static H+ have dissociation energies around 700 kJ mol-1. The corresponding B0/HA0 contacts are 1 order of magnitude weaker. When considering the effects of mobile H+, BH+/A- bond energies were found to be between these two extremes, confirming that H+ migration can significantly weaken salt bridges. Next, we examined the protein ubiquitin under collision-induced unfolding (CIU) conditions. CIU simulations were conducted using three different MD models: (i) Positive-only runs with static H+ did not allow for salt bridge formation and produced highly expanded CIU structures. (ii) Zwitterionic runs with static H+ resulted in abundant salt bridges, culminating in much more compact CIU structures. (iii) Mobile H+ simulations allowed for the dynamic formation/annihilation of salt bridges, generating CIU structures intermediate between scenarios (i) and (ii). Our results uncover that mobile H+ limit the stabilizing effects of salt bridges in the gas phase. Failure to consider the effects of mobile H+ in MD simulations will result in unrealistic outcomes under CIU conditions.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Justin H Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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27
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Ieritano C, Rickert D, Featherstone J, Honek JF, Campbell JL, Blanc JCYL, Schneider BB, Hopkins WS. The Charge-State and Structural Stability of Peptides Conferred by Microsolvating Environments in Differential Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:956-968. [PMID: 33733774 DOI: 10.1021/jasms.0c00469] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of solvent vapor in a differential mobility spectrometry (DMS) cell creates a microsolvating environment that can mitigate complications associated with field-induced heating. In the case of peptides, the microsolvation of protonation sites results in a stabilization of charge density through localized solvent clustering, sheltering the ion from collisional activation. Seeding the DMS carrier gas (N2) with a solvent vapor prevented nearly all field-induced fragmentation of the protonated peptides GGG, AAA, and the Lys-rich Polybia-MP1 (IDWKKLLDAAKQIL-NH2). Modeling the microsolvation propensity of protonated n-propylamine [PrNH3]+, a mimic of the Lys side chain and N-terminus, with common gas-phase modifiers (H2O, MeOH, EtOH, iPrOH, acetone, and MeCN) confirms that all solvent molecules form stable clusters at the site of protonation. Moreover, modeling populations of microsolvated clusters indicates that species containing protonated amine moieties exist as microsolvated species with one to six solvent ligands at all effective ion temperatures (Teff) accessible during a DMS experiment (ca. 375-600 K). Calculated Teff of protonated GGG, AAA, and Polybia-MPI using a modified two-temperature theory approach were up to 86 K cooler in DMS environments seeded with solvent vapor compared to pure N2 environments. Stabilizing effects were largely driven by an increase in the ion's apparent collision cross section and by evaporative cooling processes induced by the dynamic evaporation/condensation cycles incurred in the presence of an oscillating electric separation field. When the microsolvating partner was a protic solvent, abstraction of a proton from [MP1 + 3H]3+ to yield [MP1 + 2H]2+ was observed. This result was attributed to the proclivity of protic solvents to form hydrogen-bond networks with enhanced gas-phase basicity. Collectively, microsolvation provides analytes with a solvent "air bag," whereby charge reduction and microsolvation-induced stabilization were shown to shelter peptides from the fragmentation induced by field heating and may play a role in preserving native-like ion configurations.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Daniel Rickert
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Joshua Featherstone
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Bedrock Scientific, Milton L6T 6J9, Ontario, Canada
| | | | | | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
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28
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Conant CR, Attah IK, Garimella SVB, Nagy G, Bilbao A, Smith RD, Ibrahim YM. Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:225-236. [PMID: 33126794 PMCID: PMC8170696 DOI: 10.1021/jasms.0c00282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structures for lossless ion manipulations (SLIM) have recently enabled a powerful implementation of traveling wave ion mobility spectrometry (TWIMS) for ultrahigh resolution separations; however, experimental parameters have not been optimized, and potential significant gains may be feasible. Most TWIMS separations have utilized square-shaped waveforms applied by time-dependent voltage stepping across repeating sets of electrodes, but alternative waveforms may provide further improvements to resolution. Here, we characterize five waveforms (including square and sine) in terms of their transmission efficiency, IMS resolution, and resolving power, and explore the effects of TW amplitude and speed on the performance of each. We found, consistent with previous work, separations were generally improved with higher TW amplitudes, moderately improved by lower speeds (limited by ion "surfing" with the waves), and found decreases in signal intensity at the extremes of operating conditions. The triangle and asymmetric "ramp forward" shaped profiles were found to provide modestly greater resolution and resolving power, an observation we tentatively attribute to their relatively uniform fields and minimal low-field regions.
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Affiliation(s)
- Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aivett Bilbao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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29
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Inutan ED, Jarois DR, Lietz CB, El-Baba TJ, Elia EA, Karki S, Sampat AAS, Foley CD, Clemmer DE, Trimpin S. Comparison of gaseous ubiquitin ion structures obtained from a solid and solution matrix using ion mobility spectrometry/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8793. [PMID: 32220130 DOI: 10.1002/rcm.8793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Examining surface protein conformations, and especially achieving this with spatial resolution, is an important goal. The recently discovered ionization processes offer spatial-resolution measurements similar to matrix-assisted laser desorption/ionization (MALDI) and produce charge states similar to electrospray ionization (ESI) extending higher-mass protein applications directly from surfaces on high-performance mass spectrometers. Studying a well-interrogated protein by ion mobility spectrometry-mass spectrometry (IMS-MS) to access effects on structures using a solid vs. solvent matrix may provide insights. METHODS Ubiquitin was studied by IMS-MS using new ionization processes with commercial and homebuilt ion sources and instruments (Waters SYNAPT G2(S)) and homebuilt 2 m drift-tube instrument; MS™ sources). Mass-to-charge and drift-time (td )-measurements are compared for ubiquitin ions obtained by inlet and vacuum ionization using laserspray ionization (LSI), matrix- (MAI) and solvent-assisted ionization (SAI), respectively, and compared with those from ESI under conditions that are most comparable. RESULTS Using the same solution conditions with SYNAPT G2(S) instruments, td -distributions of various ubiquitin charge states from MAI, LSI, and SAI are similar to those from ESI using a variety of solvents, matrices, extraction voltages, a laser, and temperature only, showing subtle differences in more compact features within the elongated distribution of structures. However, on a homebuilt drift-tube instrument, within the elongated distribution of structures, both similar and different td -distributions are observed for ubiquitin ions obtained by MAI and ESI. MAI-generated ions are frequently narrower in their td -distributions. CONCLUSIONS Direct comparisons between ESI and the new ionization methods operational directly from surfaces suggest that the protein in its solution structure prior to exposure to the ionization event is either captured (frozen out) at the time of crystallization, or that the protein in the solid matrix is associated with sufficient solvent to maintain the solution structure, or, alternatively, that the observed structures are those related to what occurs in the gas phase with ESI- or MAI-generated ions and not with the solution structures.
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Affiliation(s)
- Ellen D Inutan
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Dean R Jarois
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | | | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Sarah Trimpin
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
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30
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Li A, Conant CR, Zheng X, Bloodsworth KJ, Orton DJ, Garimella SVB, Attah IK, Nagy G, Smith RD, Ibrahim YM. Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations. Anal Chem 2020; 92:14976-14982. [PMID: 33136380 DOI: 10.1021/acs.analchem.0c02829] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20, 25, and 30 V0-p). The calibration errors for the three calibrant sets (Agilent tuning mixture, polyalanine, and one assembled in-house) showed negligible differences using a sine-shaped TW waveform. Calibration errors were all within 1-2% of the drift tube ion mobility spectrometry (DTIMS) measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh-resolution multipass (long path length) SLIM TWIMS separations demonstrated improved CCS calibration for phospholipid and bile acid isomers.
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Affiliation(s)
- Ailin Li
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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31
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Naylor CN, Ridgeway ME, Park MA, Clowers BH. Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1593-1602. [PMID: 32510214 DOI: 10.1021/jasms.0c00151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A key aspect of reduced pressure ion mobility spectrometry (IMS) experiments is to identify experimental conditions that minimize the role of collisional energy transfer that allows for assessing effective ion-neutral collision cross sections of metabolites, peptides, and proteins in "native-like" or compact states. Across two separate experimental campaigns using a prototype trapped ion mobility spectrometer (TIMS) coupled to a time-of-flight mass spectrometer, we present independent findings that support the results recently published by Morsa et al. using a different set of thermometer ions (Morsa et al. Anal. Chem. 2020, 92 (6), 4573-4582). First, using five para-substituted benzylammonium ions, we conducted survival yield experiments to assess ion internal energy across different experimental settings. Results from the present set of experiments illustrate that greater ion heating occurs at lower pressures and higher voltage settings applied to the TIMS. At the "softest" settings where the benzylammonium thermometer ions have an effective average energy of 1.73 eV, we observe the majority of bradykinin in the compact state. Under more extreme operating conditions where the energy of the benzylammonium ions varies from 1.83 to 1.86 eV, the bradykinin transitions from the compact to the elongated state. In addition to independently confirming the findings of Morsa et al., we also report the mobilities for the benzylammonium parent and fragment ions using the tandem drift-tube-TIMS calibration procedure described by Naylor et al. ( J. Am. Soc. Mass Spectrom. 2019, 30 (10), 2152-2162).
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
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32
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Uppal SS, Mookherjee A, Harkewicz R, Beasley SE, Bush MF, Guttman M. High-Precision, Gas-Phase Hydrogen/Deuterium-Exchange Kinetics by Mass Spectrometry Enabled by Exchange Standards. Anal Chem 2020; 92:7725-7732. [PMID: 32368904 DOI: 10.1021/acs.analchem.0c00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mass spectrometry (MS) has become a primary tool for identifying and quantifying biological molecules. In combination with other orthogonal techniques, such as gas-phase hydrogen/deuterium exchange (gHDX), MS is also capable of probing the structure of ions. However, gHDX kinetics can depend strongly on many factors, including laboratory temperature, instrumental conditions, and instrument platform selection. These effects can lead to high variability with gHDX measurements, which has hindered the broader adoption of gHDX for structural MS. Here we introduce an approach for standardizing gHDX measurements using cosampled standards. Quantifying the exchange kinetics for analytes relative to the exchange kinetics of the standards results in greater accuracy and precision than the underlying absolute measurements. The standardization was found to be effective for several types of analytes including small molecules and intact proteins. A subset of analytes showed deviations in their standardized exchange profiles that are attributed to field heating and the concomitant conformational isomerization. Inclusion of helium during the gHDX process for collisional cooling helps mitigate such variations in exchange kinetics related to ion heating. We anticipate that the outcomes of this research will enable the broader use of gHDX in MS-based workflows for molecular identification and isomer differentiation.
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Affiliation(s)
- Sanjit S Uppal
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Abhigya Mookherjee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rick Harkewicz
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sarah E Beasley
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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33
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Urner LH, Schulze M, Maier YB, Hoffmann W, Warnke S, Liko I, Folmert K, Manz C, Robinson CV, Haag R, Pagel K. A new azobenzene-based design strategy for detergents in membrane protein research. Chem Sci 2020; 11:3538-3546. [PMID: 34109026 PMCID: PMC8152689 DOI: 10.1039/d0sc01022g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/09/2020] [Indexed: 12/02/2022] Open
Abstract
Mass spectrometry enables the in-depth structural elucidation of membrane protein complexes, which is of great interest in structural biology and drug discovery. Recent breakthroughs in this field revealed the need for design rules that allow fine-tuning the properties of detergents in solution and gas phase. Desirable features include protein charge reduction, because it helps to preserve native features of protein complexes during transfer from solution into the vacuum of a mass spectrometer. Addressing this challenge, we here present the first systematic gas-phase study of azobenzene detergents. The utility of gas-phase techniques for monitoring light-driven changes of isomer ratios and molecular properties are investigated in detail. This leads to the first azobenzene detergent that enables the native mass spectrometry analysis of membrane proteins and whose charge-reducing properties can be tuned by irradiation with light. More broadly, the presented work outlines new avenues for the high-throughput characterization of supramolecular systems and opens a new design strategy for detergents in membrane protein research.
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Affiliation(s)
- Leonhard H Urner
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Maiko Schulze
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Yasmine B Maier
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Waldemar Hoffmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
| | - Stephan Warnke
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Kristin Folmert
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Christian Manz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road OX13QZ Oxford UK
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6 14195 Berlin Germany
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Ieritano C, Featherstone J, Haack A, Guna M, Campbell JL, Hopkins WS. How Hot Are Your Ions in Differential Mobility Spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:582-593. [PMID: 31967812 DOI: 10.1021/jasms.9b00043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ions can experience significant field-induced heating in a differential mobility cell. To investigate this phenomenon, the fragmentation of several para-substituted benzylpyridinium "thermometer" ions (R = OMe, Me, F, Cl, H, CN) was monitored in a commercial differential mobility spectrometer (DMS). The internal energy of each benzylpyridinium derivative was characterized by monitoring the degree of fragmentation to obtain an effective temperature, Teff, which corresponds to a temperature consistent with treating the observed fragmentation ratio using a unimolecular dissociation rate weighted by a Boltzmann distribution at a temperature T. It was found that ions are sufficiently thermalized after initial activation from the ESI process to the temperature of the bath gas, Tbath. Once a critical field strength was surpassed, significant fragmentation of the benzylpyridinium ions was detected. At the maximum bath gas temperature (450 K) and separation voltage (SV; 4400 V) for our instrument, Teff for the benzylpyridinium derivatives ranged from 664 ± 9 K (p-OMe) to 759 ± 17 K (p-H). The extent of activation at a given SV depends on the ion's mass, degrees of freedom, (NDoF), and collision frequency as represented by the ion's collision cross section. Plots of Teff vs the product of ion mass and NDoF and the inverse of collision cross section produce strong linear relationships. This provides an attractive avenue to estimate ion temperatures at a given SV using only intrinsic properties. Moreover, experimentally determined Teff correlate with theoretically predicted Teff using with a self-consistent method based on two-temperature theory. The various instrumental and external parameters that influence Teff are additionally discussed.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Joshua Featherstone
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Alexander Haack
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Strasse 20, Wuppertal 42119, Germany
| | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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35
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France AP, Migas LG, Sinclair E, Bellina B, Barran PE. Using Collision Cross Section Distributions to Assess the Distribution of Collision Cross Section Values. Anal Chem 2020; 92:4340-4348. [DOI: 10.1021/acs.analchem.9b05130] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Aidan P. France
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Eleanor Sinclair
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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36
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MolFind 2: A Protocol for Acquiring and Integrating MS 3 Data to Improve In Silico Chemical Structure Elucidation for Metabolomics. Methods Mol Biol 2019. [PMID: 31729668 DOI: 10.1007/978-1-0716-0030-6_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Structure elucidation of metabolites (<1000 Da) in biofluids is extremely challenging due to the diversity and complexity of chemical structure space. Generally, due to lack of reference tandem mass data (MS2), in silico fragmenters are used to rank candidates acquired from chemical databases as a function on how well they explain an experimental collision-induced dissociation spectrum. However, multistage fragmentation data (i.e., MS3) have not been adequately utilized in current metabolomics structure elucidation pipelines. To address this shortcoming, here we describe an experimental (nontargeted direct infusion ion mobility-mass spectrometry-based) and computational workflow to acquire and utilize multistage mass (MS3) spectrometry data for database-assisted structure elucidation.
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37
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Han JY, Choi TS, Heo CE, Son MK, Kim HI. Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase. MASS SPECTROMETRY REVIEWS 2019; 38:483-500. [PMID: 31021441 DOI: 10.1002/mas.21596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.
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Affiliation(s)
- Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | - Chae Eun Heo
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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38
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Historical, current and future developments of travelling wave ion mobility mass spectrometry: A personal perspective. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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39
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Dodds JN, Baker ES. Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2185-2195. [PMID: 31493234 PMCID: PMC6832852 DOI: 10.1007/s13361-019-02288-2] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 05/07/2023]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.
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Affiliation(s)
- James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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40
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Wojcik R, Nagy G, Attah IK, Webb IK, Garimella SVB, Weitz KK, Hollerbach A, Monroe ME, Ligare MR, Nielson FF, Norheim RV, Renslow RS, Metz TO, Ibrahim YM, Smith RD. SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes. Anal Chem 2019; 91:11952-11962. [PMID: 31450886 PMCID: PMC7188075 DOI: 10.1021/acs.analchem.9b02808] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400-600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason-Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization.
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Affiliation(s)
- Roza Wojcik
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac. K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ian K. Webb
- Department of Chemistry, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Adam Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Marshall R. Ligare
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Felicity F. Nielson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Randolph V. Norheim
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ryan S. Renslow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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41
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Eldrid C, Ujma J, Kalfas S, Tomczyk N, Giles K, Morris M, Thalassinos K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal Chem 2019; 91:7554-7561. [PMID: 31117399 PMCID: PMC7006968 DOI: 10.1021/acs.analchem.8b05641] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Ion
mobility mass spectrometry (IM-MS) allows separation of native
protein ions into “conformational families”. Increasing
the IM resolving power should allow finer structural information to
be obtained and can be achieved by increasing the length of the IM
separator. This, however, increases the time that protein ions spend
in the gas phase and previous experiments have shown that the initial
conformations of small proteins can be lost within tens of milliseconds.
Here, we report on investigations of protein ion stability using a
multipass traveling wave (TW) cyclic IM (cIM) device. Using this device,
minimal structural changes were observed for Cytochrome C after hundreds
of milliseconds, while no changes were observed for a larger multimeric
complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF)
also enables complex tandem IM experiments to be performed, which
were used to obtain more detailed collision-induced unfolding pathways
for Cytochrome C. The instrument geometry provides unique capabilities
with the potential to expand the field of protein analysis via IM-MS.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Jakub Ujma
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Symeon Kalfas
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Nick Tomczyk
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Kevin Giles
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Mike Morris
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College , University of London , London , WC1E 7HX , United Kingdom
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42
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Dixit SM, Ruotolo BT. A Semi-Empirical Framework for Interpreting Traveling Wave Ion Mobility Arrival Time Distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:956-966. [PMID: 30815838 DOI: 10.1007/s13361-019-02133-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
The inherent structural heterogeneity of biomolecules is an important biophysical property that is essential to their function, but is challenging to characterize experimentally. We present a workflow that rapidly and quantitatively assesses the conformational heterogeneity of peptides and proteins in the gas phase using traveling wave ion mobility (TWIM) arrival time distributions (ATDs). We have established a set of semi-empirical equations that model the TWIM ATD peak width and resolution across a wide range of wave amplitudes (V) and wave velocities (v). In addition, a conformational broadening parameter, δ, can be extracted from this analysis that reports on the contribution of conformational heterogeneity to the broadening of TWIM ATD peak width during ion mobility separation. We use this δ value to evaluate the conformational heterogeneity of a set of helical peptides, and our analysis correlates well with previous peak width observations reported for these ions. Furthermore, we use molecular dynamics simulations to independently investigate the general flexibility of these peptides in the gas phase, and generate similar trends found in experimental TWIM data. Finally, we extended our analysis to Avidin, a 64-kDa homotetramer, and quantify the structural heterogeneity of this intact complex using TWIM ATD data as a function of cross-linking. We observe an initial reduction in δ values as a function of cross-linker concentration, demonstrating the sensitivity of our δ value analysis to changes in flexibility of the assembly.
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Affiliation(s)
- Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA.
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43
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Lim D, Park Y, Chang R, Ahmed A, Kim S. Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:650-656. [PMID: 30710409 DOI: 10.1002/rcm.8400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains. METHODS In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values. RESULTS The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered. CONCLUSIONS The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.
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Affiliation(s)
- Dongwan Lim
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yunjae Park
- Department of Chemistry, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
- Green Nano Center, Department of Chemistry, Daegu, 41566, Republic of Korea
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44
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Kirk AT, Bohnhorst A, Raddatz CR, Allers M, Zimmermann S. Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments. Anal Bioanal Chem 2019; 411:6229-6246. [PMID: 30957205 DOI: 10.1007/s00216-019-01807-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
Abstract
With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.
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Affiliation(s)
- Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany.
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
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45
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Oranzi NR, Kemperman RHJ, Wei MS, Petkovska VI, Granato SW, Rochon B, Kaszycki J, La Rotta A, Jeanne Dit Fouque K, Fernandez-Lima F, Yost RA. Measuring the Integrity of Gas-Phase Conformers of Sodiated 25-Hydroxyvitamin D3 by Drift Tube, Traveling Wave, Trapped, and High-Field Asymmetric Ion Mobility. Anal Chem 2019; 91:4092-4099. [DOI: 10.1021/acs.analchem.8b05723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nicholas R. Oranzi
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | | | - Michael S. Wei
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
| | | | - Scott W. Granato
- Axalta Coating Systems, Philadelphia, Pennsylvania, United States
| | - Benjamin Rochon
- Axalta Coating Systems, Philadelphia, Pennsylvania, United States
| | - Julia Kaszycki
- Excellims Corporation, Acton, Massachusetts, United States
| | | | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States
- Biomolecular Science Institute, Florida International University, Miami, Florida, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States
- Biomolecular Science Institute, Florida International University, Miami, Florida, United States
| | - Richard A. Yost
- Department of Chemistry, University of Florida, Gainesville, Florida, United States
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46
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Paul M, Detmar E, Schlangen M, Breugst M, Neudörfl JM, Schwarz H, Berkessel A, Schäfer M. Intermediates of N-Heterocyclic Carbene (NHC) Dimerization Probed in the Gas Phase by Ion Mobility Mass Spectrometry: C-H⋅⋅⋅:C Hydrogen Bonding Versus Covalent Dimer Formation. Chemistry 2019; 25:2511-2518. [PMID: 30488654 DOI: 10.1002/chem.201803641] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/27/2018] [Indexed: 11/06/2022]
Abstract
N-Heterocyclic carbenes (NHCs, :C) can interact with azolium salts (C-H+ ) by either forming a hydrogen-bonded aggregate (CHC+ ) or a covalent C-C bond (CCH+ ). In this study, the intramolecular NHC-azolium salt interactions of aromatic imidazolin-2-ylidenes and saturated imidazolidin-2-ylidenes have been investigated in the gas phase by traveling wave ion mobility mass spectrometry (TW IMS) and DFT calculations. The TW IMS experiments provided evidence for the formation of these important intermediates in the gas phase, and they identified the predominant aggregation mode (hydrogen bond vs. covalent C-C) as a function of the nature of the interacting carbene-azolium pairs.
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Affiliation(s)
- Mathias Paul
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Eric Detmar
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Maria Schlangen
- Institute of Chemistry, Technical University Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Martin Breugst
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Helmut Schwarz
- Institute of Chemistry, Technical University Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Albrecht Berkessel
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Mathias Schäfer
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
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47
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Xia Z, DeGrandchamp JB, Williams ER. Native mass spectrometry beyond ammonium acetate: effects of nonvolatile salts on protein stability and structure. Analyst 2019; 144:2565-2573. [DOI: 10.1039/c9an00266a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Structures and stabilities of proteins investigated with native mass spectrometry can be affected by nonvolatile salts, including Tris buffer, in solution.
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Affiliation(s)
- Zijie Xia
- Department of Chemistry
- University of California
- Berkeley
- USA
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48
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Tejada-Casado C, Hernández-Mesa M, Monteau F, Lara FJ, Olmo-Iruela MD, García-Campaña AM, Le Bizec B, Dervilly-Pinel G. Collision cross section (CCS) as a complementary parameter to characterize human and veterinary drugs. Anal Chim Acta 2018; 1043:52-63. [DOI: 10.1016/j.aca.2018.09.065] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 12/27/2022]
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49
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Ouyang H, Bo T, Zhang Z, Guo X, He M, Li J, Yang S, Ma X, Feng Y. Ion mobility mass spectrometry with molecular modelling to reveal bioactive isomer conformations and underlying relationship with isomerization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1931-1940. [PMID: 30151930 DOI: 10.1002/rcm.8271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/21/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In medicine and drug development, molecular modelling is an important tool. It is attractive to develop a platform connecting the theoretical structural modelling and the results from experimental measurement. In addition, the separation and structural analysis of bioactive constituent isomers are still challenging tasks. METHODS Drift tube ion mobility (IM) mass spectrometry (MS) provides the experimental collision cross section (CCS) which contains the structural information. The experimental CCS can be compared with the calculated CCS of the molecular modelling structures. This technique is especially useful for bioactive constituents in herbal medicine because active isomers with the same chemical formula are common in these samples. IM helps separate and identify these isomers and reveals details about their structures and conformations. RESULTS Two model bioactive constituents, caffeoylquinic acids (CQAs) and dicaffeoylquinic acids (di-CQAs), were selected to systematically investigate the influence of solution, ion source conditions and ion heating on the isomer CCS distributions. By comparing the calculated CCS with the experimental value, we identified the favorable conformations of CQAs. The most compact conformation of a CQA was less likely to isomerize than the more extended conformation. It was found that the isomerization tendency was in accord with the conformation favorability. CONCLUSIONS This study offers an effective approach to predict and demystify the conformation and isomerization of the active constituents in herbal medicines.
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Affiliation(s)
- Hui Ouyang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Tao Bo
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Zhengxiang Zhang
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Xinqiu Guo
- Ming De Tian Sheng Biotech Inc., Changping Campus of Peking University, Beijing, 102200, China
| | - Mingzhen He
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Junmao Li
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Shilin Yang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
| | - Xin Ma
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Yulin Feng
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
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Xu Z, Li J, Chen A, Ma X, Yang S. A new retrospective, multi-evidence veterinary drug screening method using drift tube ion mobility mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1141-1148. [PMID: 29723930 DOI: 10.1002/rcm.8154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/14/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE The retrospectivity (the ability to retrospect to a previously unknown compound in raw data) is very meaningful for food safety and risk assessment when facing new emerging drugs. Accurate mass and retention time based screening may lead false positive and false negative results so new retrospective, reliable platform is desirable. METHODS Different concentration levels of standards with and without matrix were analyzed using ion mobility (IM)-quadrupole-time-of-flight (Q-TOF) for collecting retrospective accurate mass, retention time, drift time and tandem MS evidence for identification in a single experiment. The isomer separation ability of IM and the four-dimensional (4D) feature abundance quantification abilities were evaluated for veterinary drugs for the first time. RESULTS The sensitivity of the IM-Q-TOF workflow was obviously higher than that of the traditional database searching algorithm [find by formula (FbF) function] for Q-TOF. In addition, the IM-Q-TOF workflow contained most of the results from FbF and removed the false positive results. Some isomers were separated by IM and the 4D feature abundance quantitation removed interference with similar accurate mass and showed good linearity. CONCLUSION A new retrospective, multi-evidence platform was built for veterinary drug screening in a single experiment. The sensitivity was significantly improved and the data can be used for quantification. The platform showed its potential to be used for food safety and risk assessment.
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Affiliation(s)
- Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture, Beijing, 100081, China
| | | | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture, Beijing, 100081, China
| | - Xin Ma
- Agilent Technologies, Beijing, 100102, China
| | - Shuming Yang
- Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture, Beijing, 100081, China
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