1
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Webb IK. Perspective: The complex relationship between charge, mobility, and gas-phase protein structure. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5013. [PMID: 38605450 DOI: 10.1002/jms.5013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Ion mobility spectrometry coupled to mass spectrometry (IMS/MS) is a widely used tool for biomolecular separations and structural elucidation. The application of IMS/MS has resulted in exciting developments in structural proteomics and genomics. This perspective gives a brief background of the field, addresses some of the important issues in making structural measurements, and introduces complementary techniques.
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Affiliation(s)
- Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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2
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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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3
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Muller HB, Scholl G, Far J, De Pauw E, Eppe G. Sliding Windows in Ion Mobility (SWIM): A New Approach to Increase the Resolving Power in Trapped Ion Mobility-Mass Spectrometry Hyphenated with Chromatography. Anal Chem 2023; 95:17586-17594. [PMID: 37976440 DOI: 10.1021/acs.analchem.3c03039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Over the past decade, the separation efficiency achieved by linear IMS instruments has increased substantially, with state-of-the-art IM technologies, such as the trapped ion mobility (TIMS), the cyclic traveling wave ion mobility (cTWIMS), and the structure for lossless ion manipulation (SLIM) platforms commonly demonstrating resolving powers in excess of 200. However, for complex sample analysis that require front end separation, the achievement of such high resolving power in TIMS is significantly hampered, since the ion mobility range must be broad enough to analyze all the classes of compounds of interest, whereas the IM analysis time must be short enough to cope with the time scale of the preseparation technique employed. In this paper, we introduce the concept of sliding windows in ion mobility (SWIM) for chromatography hyphenated TIMS applications that bypasses the need to use a wide and fixed IM range by using instead narrow and mobile ion mobility windows that adapt to the analytes' ion mobility during chromatographic separation. GC-TIMS-MS analysis of a mixture of 174 standards from several halogenated persistent organic pollutant (POP) classes, including chlorinated and brominated dioxins, biphenyls, and PBDEs, demonstrated that the average IM resolving power could be increased up to 40% when the SWIM mode was used, thereby greatly increasing the method selectivity for the analysis of complex samples.
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Affiliation(s)
- Hugo B Muller
- Mass Spectrometry Laboratory, University of Liège, Liège 4000, Belgium
| | - Georges Scholl
- Mass Spectrometry Laboratory, University of Liège, Liège 4000, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, University of Liège, Liège 4000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, University of Liège, Liège 4000, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, University of Liège, Liège 4000, Belgium
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4
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Canellas E, Vera P, Nerin C, Goshawk J, Dreolin N. Migration of contaminants from printed masks for children to saliva simulant using liquid chromatography coupled to ion mobility-time of flight-mass spectrometry and gas chromatography-mass spectrometry. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115644. [PMID: 37924803 DOI: 10.1016/j.ecoenv.2023.115644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023]
Abstract
The COVID-19 pandemic has led to children using polymeric FFP2 and polymeric surgical masks on a daily basis. Children often bite and suck on such masks as they wear them closed to their mouths. In this work, the migration of contaminants from printed and unprinted children`s masks to a saliva simulant has been studied. Liquid chromatography coupled to ion-mobility quadrupole time-of-flight mass spectrometry has been used for the detection and identification of non-volatile migrants. An orthogonal projection to latent structures - discriminant analysis (OPLS-DA) was applied to compare the data from the printed masks against the data from the unprinted ones. Headspace solid phase microextraction coupled to gas chromatography mass spectrometry was used to assess the migration of volatile compounds. Thirteen compounds were found in the masks with concentrations ranging from 5 ng/g to 254 ng/g. Toluene, chlorobenzene, irganox 1076 and 2-(2-butoxyethoxy)ethyl acetate were all found to migrate from the masks studied. Moreover, differences between the migrants from printed and unprinted FFP2 masks were found. Octocrylene, 4-(dimethylamine)benzoate, methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate and tris(3-methylphenyl)phosphate were found to migrate only from printed masks. Toluene that migrated from all the masks studied and tris(3-methylphenyl)phosphate, that migrated only from printed masks, have been listed as hazardous priority substances.
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Affiliation(s)
- Elena Canellas
- GUIA Group, Department of Analytical Chemistry, University of Zaragoza, I3A, María de Luna, 3, 50018 Zaragoza, Spain.
| | - Paula Vera
- GUIA Group, Department of Analytical Chemistry, University of Zaragoza, I3A, María de Luna, 3, 50018 Zaragoza, Spain
| | - Cristina Nerin
- GUIA Group, Department of Analytical Chemistry, University of Zaragoza, I3A, María de Luna, 3, 50018 Zaragoza, Spain
| | - Jeff Goshawk
- Waters Corporation, Wilmslow, Stamford Avenue, Altrincham Road, SK9 4AX, United Kingdom
| | - Nicola Dreolin
- Waters Corporation, Wilmslow, Stamford Avenue, Altrincham Road, SK9 4AX, United Kingdom
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5
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Haack A, Ieritano C, Hopkins WS. MobCal-MPI 2.0: an accurate and parallelized package for calculating field-dependent collision cross sections and ion mobilities. Analyst 2023. [PMID: 37376881 DOI: 10.1039/d3an00545c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Ion mobility spectrometry (IMS), which can be employed as either a stand-alone instrument or coupled to mass spectrometry, has become an important tool for analytical chemistry. Because of the direct relation between an ion's mobility and its structure, which is intrinsically related to its collision cross section (CCS), IMS techniques can be used in tandem with computational tools to elucidate ion geometric structure. Here, we present MobCal-MPI 2.0, a software package that demonstrates excellent accuracy (RMSE 2.16%) and efficiency in calculating low-field CCSs via the trajectory method (≤30 minutes on 8 cores for ions with ≤70 atoms). MobCal-MPI 2.0 expands on its predecessor by enabling the calculation of high-field mobilities through the implementation of the 2nd order approximation to two-temperature theory (2TT). By further introducing an empirical correction to account for deviations between 2TT and experiment, MobCal-MPI 2.0 can compute accurate high-field mobilities that exhibit a mean deviation of <4% from experimentally measured values. Moreover, the velocities used to sample ion-neutral collisions were updated from a weighted to a linear grid, enabling the near-instantaneous evaluation of mobility/CCS at any effective temperature from a single set of N2 scattering trajectories. Several enhancements made to the code are also discussed, including updates to the statistical analysis of collision event sampling and benchmarking of overall performance.
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Affiliation(s)
- Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
| | - Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
- Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada.
- Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, 999077, Hong Kong
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6
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Harrilal CP, Garimella SVB, Chun J, Devanathan N, Zheng X, Ibrahim YM, Larriba-Andaluz C, Schenter G, Smith RD. The Role of Ion Rotation in Ion Mobility: Ultrahigh-Precision Prediction of Ion Mobility Dependence on Ion Mass Distribution and Translational to Rotational Energy Transfer. J Phys Chem A 2023. [PMID: 37330993 DOI: 10.1021/acs.jpca.3c01264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The role of ion rotation in determining ion mobilities is explored using the subtle gas phase ion mobility shifts based on differences in ion mass distributions between isotopomer ions that have been observed with ion mobility spectrometry (IMS) measurements. These mobility shifts become apparent for IMS resolving powers on the order of ∼1500 where relative mobilities (or alternatively momentum transfer collision cross sections; Ω) can be measured with a precision of ∼10 ppm. The isotopomer ions have identical structures and masses, differing only in their internal mass distributions, and their Ω differences cannot be predicted by widely used computational approaches, which ignore the dependence of Ω on the ion's rotational properties. Here, we investigate the rotational dependence of Ω, which includes changes to its collision frequency due to thermal rotation as well as the coupling of translational to rotational energy transfer. We show that differences in rotational energy transfer during ion-molecule collisions provide the major contribution to isotopomer ion separations, with only a minor contribution due to an increase in collision frequency due to ion rotation. Modeling including these factors allowed for differences in Ω to be calculated that precisely mirror the experimental separations. These findings also highlight the promise of pairing high-resolution IMS measurements with theory and computation for improved elucidation of subtle structural differences between ions.
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Affiliation(s)
- Christopher P Harrilal
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Nikhil Devanathan
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Carlos Larriba-Andaluz
- Department of Mechanical and Energy Engineering, IUPUI, Indianapolis, Indiana 46202, United States
| | - Gregory Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
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7
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Cajahuaringa S, Caetano DLZ, Zanotto LN, Araujo G, Skaf MS. MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. J Chem Inf Model 2023; 63:3557-3566. [PMID: 37184925 PMCID: PMC10269586 DOI: 10.1021/acs.jcim.3c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.
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Affiliation(s)
- Samuel Cajahuaringa
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Daniel L. Z. Caetano
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Leandro N. Zanotto
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Guido Araujo
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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8
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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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9
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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10
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Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
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Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
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11
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Gandhi VD, Hua L, Chen X, Latif M, Larriba-Andaluz C. A Critical Review of the two-temperature theory and the derivation of matrix elements. High field Ion mobility and energy calculation for all-atom structures in light gases using a 12-6-4 potential. TALANTA OPEN 2023. [DOI: 10.1016/j.talo.2023.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
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12
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Rehfeldt T, Gabriels R, Bouwmeester R, Gessulat S, Neely BA, Palmblad M, Perez-Riverol Y, Schmidt T, Vizcaíno JA, Deutsch EW. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. J Proteome Res 2023; 22:632-636. [PMID: 36693629 PMCID: PMC9903315 DOI: 10.1021/acs.jproteome.2c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the high levels of data reduction that occur between raw data and machine learning-ready data. Since predictive proteomics is an emerging field, when predicting peptide behavior in LC-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility. For this reason we introduce ProteomicsML, an online resource for proteomics-based data sets and tutorials across most of the currently explored physicochemical peptide properties. This community-driven resource makes it simple to access data in easy-to-process formats, and contains easy-to-follow tutorials that allow new users to interact with even the most advanced algorithms in the field. ProteomicsML provides data sets that are useful for comparing state-of-the-art machine learning algorithms, as well as providing introductory material for teachers and newcomers to the field alike. The platform is freely available at https://www.proteomicsml.org/, and we welcome the entire proteomics community to contribute to the project at https://github.com/ProteomicsML/ProteomicsML.
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Affiliation(s)
- Tobias
G. Rehfeldt
- Institute
for Mathematics and Computer Science, University
of Southern Denmark, 5000 Odense, Denmark
| | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, Ghent 9052, Belgium,Department
of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Robbin Bouwmeester
- VIB-UGent
Center for Medical Biotechnology, VIB, Ghent 9052, Belgium,Department
of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | | | - Benjamin A. Neely
- National
Institute of Standards and Technology, Charleston, South Carolina 29412, United States
| | - Magnus Palmblad
- Center for
Proteomics and Metabolomics, Leiden University
Medical Center, 2300 RC Leiden, The Netherlands
| | - Yasset Perez-Riverol
- European
Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Juan Antonio Vizcaíno
- European
Molecular Biology Laboratory, European Bioinformatics
Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom,Juan
Antonio Vizcaíno: , Phone: +44 (0) 1223 492686
| | - Eric W. Deutsch
- Institute
for Systems Biology, Seattle, Washington 98109, United States,Eric Deutsch: ,
Phone: 206-732-1200, Fax: 206-732-1299
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13
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Haack A, Hopkins WS. Kinetics in DMS: Modeling Clustering and Declustering Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2250-2262. [PMID: 36331115 DOI: 10.1021/jasms.2c00224] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Differential mobility spectrometry (DMS) uses high-frequency oscillating electrical fields to harness the differential mobility of ions for separating complex sample mixtures prior to detection. To increase the resolving power, a dynamic microsolvation environment is often created by introducing solvent vapors. Here, relatively large clusters are formed at low-field conditions which then evaporate to form smaller clusters at high-field conditions. The kinetics of these processes as the electrical field strength oscillates are not well studied. Here, we develop a computational framework to investigate how the different reactions (cluster association, cluster dissociation, and fast conformational changes) behave at different field strengths. We aim to better understand these processes, their effect on experimental outcomes, and whether DMS model accuracy is improved via incorporating their description. We find that cluster association and dissociation reactions for typical ion-solvent pairs are fast compared to the time scale of the varying separation fields usually used. However, low solvent concentration, small dipole moments, and strong ion-solvent binding can result in reaction rates small enough that a lag is observed in the ion's DMS response. This can yield differences of several volts in the compensation voltages required to correct ion trajectories for optimal transmission. We also find that the proposed kinetic approach yields generally better agreement with experiment than using a modified Boltzmann weighting scheme. Thus, this work provides insights into the chemical dynamics occurring within the DMS cell while also increasing the accuracy of dispersion plot predictions.
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Affiliation(s)
- Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ONN2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Ave W, Waterloo, ONN2L 3G1, Canada
- Watermine Innovation, Waterloo, OntarioN0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories999077, Hong Kong
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14
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Dubrovskii SA, Balabaev NK. Molecular Dynamics Simulation of the Behavior of Protonated Poly(ethylene oxide)s in Drift Tube Experiments. POLYMER SCIENCE SERIES A 2022. [DOI: 10.1134/s0965545x22700201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Ieritano C, Hopkins WS. The hitchhiker's guide to dynamic ion-solvent clustering: applications in differential ion mobility spectrometry. Phys Chem Chem Phys 2022; 24:20594-20615. [PMID: 36000315 DOI: 10.1039/d2cp02540j] [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
This article highlights the fundamentals of ion-solvent clustering processes that are pertinent to understanding an ion's behaviour during differential mobility spectrometry (DMS) experiments. We contrast DMS with static-field ion mobility, where separation is affected by mobility differences under the high-field and low-field conditions of an asymmetric oscillating electric field. Although commonly used in mass spectrometric (MS) workflows to enhance signal-to-noise ratios and remove isobaric contaminants, the chemistry and physics that underpins the phenomenon of differential mobility has yet to be fully fleshed out. Moreover, we are just now making progress towards understanding how the DMS separation waveform creates a dynamic clustering environment when the carrier gas is seeded with the vapour of a volatile solvent molecule (e.g., methanol). Interestingly, one can correlate the dynamic clustering behaviour observed in DMS experiments with gas-phase and solution-phase molecular properties such as hydrophobicity, acidity, and solubility. However, to create a generalized, global model for property determination using DMS data one must employ machine learning. In this article, we provide a first-principles description of differential ion mobility in a dynamic clustering environment. We then discuss the correlation between dynamic clustering propensity and analyte physicochemical properties and demonstrate that analytes exhibiting similar ion-solvent interactions (e.g., charge-dipole) follow well-defined trends with respect to DMS clustering behaviour. Finally, we describe how supervised machine learning can be used to create predictive models of molecular properties using DMS data. We additionally highlight open questions in the field and provide our perspective on future directions that can be explored.
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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, 17W Hong Kong Science Park, New Territories, 999077, Hong Kong
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16
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Yang H, Ding D, Skyttä A, Cai R, Kulmala M, Kangasluoma J. Electrical Mobility as an Indicator for Flexibly Deducing the Kinetics of Nanoparticle Evaporation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:8794-8800. [PMID: 35655937 PMCID: PMC9150095 DOI: 10.1021/acs.jpcc.2c02858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Condensation and evaporation of vapor species on nanoparticle surfaces drive the aerosol evolution in various industrial/atmospheric systems, but probing these transient processes is challenging due to related time and length scales. Herein, we present a novel methodology for deducing nanoparticle evaporation kinetics using electrical mobility as a natural size indicator. Monodispersed nanoparticles are fed to a differential mobility analyzer which serves simultaneously as an evaporation flowtube and an instrument for measuring the electrical mobility, realizing measurements of evaporation processes with time scales comparable to the instrument response time. A theoretical framework is derived for deducing the evaporation kinetics from instrument responses through analyzing the nanoparticle trajectory and size-mobility relationship, which considers the coupled mass and heat transfer effect and is applicable to the whole Knudsen number range. The methodology is demonstrated against evaporation but can potentially be extended to condensation and other industrial/atmospheric processes involving rapid size change of nanoparticles.
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17
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Haack A, Bissonnette JR, Ieritano C, Hopkins WS. Improved First-Principles Model of Differential Mobility Using Higher Order Two-Temperature Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:535-547. [PMID: 35099948 DOI: 10.1021/jasms.1c00354] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Differential mobility spectrometry is a separation technique that may be applied to a variety of analytes ranging from small molecule drugs to peptides and proteins. Although rudimentary theoretical models of differential mobility exist, these models are often only applied to small molecules and atomic ions without considering the effects of dynamic microsolvation. Here, we advance our theoretical description of differential ion mobility in pure N2 and microsolvating environments by incorporating higher order corrections to two-temperature theory (2TT) and a pseudoequilibrium approach to describe ion-neutral interactions. When comparing theoretical predictions to experimentally measured dispersion plots of over 300 different compounds, we find that higher order corrections to 2TT reduce errors by roughly a factor of 2 when compared to first order. Model predictions are accurate especially for pure N2 environments (mean absolute error of 4 V at SV = 4000 V). For strongly clustering environments, accurate thermochemical corrections for ion-solvent clustering are likely required to reliably predict differential ion mobility behavior. Within our model, general trends associated with clustering strength, solvent vapor concentration, and background gas temperature are well reproduced, and fine structure visible in some dispersion plots is captured. These results provide insight into the dynamic ion-solvent clustering process that underpins the phenomenon of differential ion mobility.
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Affiliation(s)
- Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, ON N2L 3G1, Canada
| | - Justine R Bissonnette
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, ON N2L 3G1, Canada
| | - Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, ON N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, ON N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
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18
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Bianco A, Neefjes I, Alfaouri D, Vehkamäki H, Kurtén T, Ahonen L, Passananti M, Kangasluoma J. Separation of isomers using a differential mobility analyser (DMA): Comparison of experimental vs modelled ion mobility. Talanta 2022; 243:123339. [DOI: 10.1016/j.talanta.2022.123339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/01/2023]
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19
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Williamson DL, Bergman AE, Heider EC, Nagy G. Experimental Measurements of Relative Mobility Shifts Resulting from Isotopic Substitutions with High-Resolution Cyclic Ion Mobility Separations. Anal Chem 2022; 94:2988-2995. [PMID: 35107996 DOI: 10.1021/acs.analchem.1c05240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, we report on the experimental measurements for estimated relative mobility shifts caused by changes in mass distribution from isotopic substitutions in isotopologues and isotopomers with high-resolution cyclic ion mobility separations. By utilizing unlabeled and fully labeled isotopologues with the same isotopic substitutions (i.e., 2H or 13C), we created a highly precise mobility scale for each set analyzed to determine the magnitude of such mass distribution shifts and thus calculate estimated deviations from expected, theoretical reduced mass contributions. We observed relative mobility shifts in various isotopologues (e.g., hexadecyltrimethylammonium, sucrose, and palmitic acid species) that deviated from reduced mass theory, according to the Mason-Schamp relationship, ranging in estimated magnitude from ∼0.007% up to ∼0.1% in relative mobility. More interestingly, it was found that two deuterated palmitic acid isotopomers also differed by ∼0.03% from one another in their respective relative mobility shifts. Our results are the first report of isotopologue and isotopomer separations on a commercially available cyclic ion mobility spectrometry-mass spectrometry platform. We envision that our presented mobility scale methodology will have broad applicability in studying the effect of mass distribution changes from isotopic substitutions in other biomolecules and help pave the way for the improvement of ion mobility theory and collision cross section calculators.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Addison E Bergman
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Emily C Heider
- Department of Chemistry, Utah Valley University, 800 W University Parkway, PS-009G, Orem, Utah 84058, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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20
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Harrilal CP, Gandhi VD, Nagy G, Chen X, Buchanan MG, Wojcik R, Conant CR, Donor MT, Ibrahim YM, Garimella SVB, Smith RD, Larriba-Andaluz C. Measurement and Theory of Gas-Phase Ion Mobility Shifts Resulting from Isotopomer Mass Distribution Changes. Anal Chem 2021; 93:14966-14975. [PMID: 34726890 DOI: 10.1021/acs.analchem.1c01736] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unanticipated discovery of recent ultra-high-resolution ion mobility spectrometry (IMS) measurements revealing that isotopomers─compounds that differ only in the isotopic substitution sites─can be separated has raised questions as to the physical basis for their separation. A study comparing IMS separations for two isotopomer sets in conjunction with theory and simulations accounting for ion rotational effects provides the first-ever prediction of rotation-mediated shifts. The simulations produce observable mobility shifts due to differences in gas-ion collision frequency and translational-to-rotational energy transfer. These differences can be attributed to distinct changes in the moment of inertia and center of mass between isotopomers. The simulations are in broad agreement with the observed experiments and consistent with relative mobility differences between isotopomers. These results provide a basis for refining IMS theory and a new foundation to obtain additional structural insights through IMS.
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Affiliation(s)
- Christopher P Harrilal
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - 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 Street, Indianapolis, Indiana 46202, United States
| | - Gabe Nagy
- Chemistry Department, University of Utah, Salt Lake City, Utah 84112, United States
| | - Xi Chen
- 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 Street, Indianapolis, Indiana 46202, United States
| | - Michael G Buchanan
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
| | - Roza Wojcik
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Micah T Donor
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Carlos Larriba-Andaluz
- Department of Mechanical and Energy Engineering, IUPUI, 723 W. Michigan Street, Indianapolis, Indiana 46202, United States
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21
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Niedner‐Schatteburg G, Kappes MM. Advancing Inorganic Coordination Chemistry by Spectroscopy of Isolated Molecules: Methods and Applications. Chemistry 2021; 27:15027-15042. [PMID: 34636096 PMCID: PMC8596414 DOI: 10.1002/chem.202102815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 12/14/2022]
Abstract
A unique feature of the work carried out in the Collaborative Research Center 3MET continues to be its emphasis on innovative, advanced experimental methods which hyphenate mass-selection with further analytical tools such as laser spectroscopy for the study of isolated molecular ions. This allows to probe the intrinsic properties of the species of interest free of perturbing solvent or matrix effects. This review explains these methods and uses examples from past and ongoing 3MET studies of specific classes of multicenter metal complexes to illustrate how coordination chemistry can be advanced by applying them. As a corollary, we will show how the challenges involved in providing well-defined, for example monoisomeric, samples of the molecular ions have helped to further improve the methods themselves thus also making them applicable to many other areas of chemistry.
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Affiliation(s)
| | - Manfred M. Kappes
- Institute of Physical Chemistry and Institute of NanotechnologyKarlsruhe Institute of Technology (KIT)76128KarlsruheGermany
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22
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Dubrovskii SA, Balabaev NK. Simulation of the Drift of a Macromolecular Ion in a Gas under the Action of an Electric Field. POLYMER SCIENCE SERIES A 2021. [DOI: 10.1134/s0965545x21060031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Gandhi VD, Larriba-Andaluz C. Predicting ion mobility as a function of the electric field for small ions in light gases. Anal Chim Acta 2021; 1184:339019. [PMID: 34625252 DOI: 10.1016/j.aca.2021.339019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/07/2021] [Accepted: 08/30/2021] [Indexed: 12/01/2022]
Abstract
High resolution mobility devices such as Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) and Differential Mobility spectrometers (DMS) use strong electric fields to gas concentration ratios, E/N, to separate ions in the gas phase. While extremely successful, their empirical results show a non-linear, ion-dependent relation between mobility K and E/N that is difficult to characterize. The one-temperature theory Mason-Schamp equation, which is the most widely used ion mobility equation, unfortunately, cannot capture this behavior. When the two-temperature theory is used, it can be shown that the K-E/N behavior can be followed quite closely numerically by equating the effect of increasing the field to an increase in the ion temperature. This is attempted here for small ions in a Helium gas environment showing good agreement over the whole field range. To improve the numerical characterization, the Lennard-Jones (L-J) potentials may be optimized. This is attempted for Carbon, Hydrogen, Oxygen and Nitrogen at different degrees of theory up to the fourth approximation, which is assumed to be exact. The optimization of L-J improves the accuracy yielding errors of about 3% on average. The fact that a constant set of L-J potentials work for the whole range of E/N and for several molecules, also suggests that inelastic collisions can be circumvented in calculations for He. The peculiar K-E/N hump behaviors are studied, and whether mobility increases or decreases with E/N is shown to derive from a competition between relative kinetic energy and the interaction potentials.
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Affiliation(s)
- Viraj D Gandhi
- Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, 47907, Indiana, United States; Mechanical Engineering, Indiana University Purdue University - Indianapolis, 723 W Michigan Street, Indianapolis, 46202, Indiana, United States
| | - Carlos Larriba-Andaluz
- Mechanical Engineering, Indiana University Purdue University - Indianapolis, 723 W Michigan Street, Indianapolis, 46202, Indiana, United States.
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24
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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25
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Ieritano C, Campbell JL, Hopkins WS. Predicting differential ion mobility behaviour in silico using machine learning. Analyst 2021; 146:4737-4743. [PMID: 34212943 DOI: 10.1039/d1an00557j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although there has been a surge in popularity of differential mobility spectrometry (DMS) within analytical workflows, determining separation conditions within the DMS parameter space still requires manual optimization. A means of accurately predicting differential ion mobility would benefit practitioners by significantly reducing the time associated with method development. Here, we report a machine learning (ML) approach that predicts dispersion curves in an N2 environment, which are the compensation voltages (CVs) required for optimal ion transmission across a range of separation voltages (SVs) between 1500 to 4000 V. After training a random-forest based model using the DMS information of 409 cationic analytes, dispersion curves were reproduced with a mean absolute error (MAE) of ≤ 2.4 V, approaching typical experimental peak FWHMs of ±1.5 V. The predictive ML model was trained using only m/z and ion-neutral collision cross section (CCS) as inputs, both of which can be obtained from experimental databases before being extensively validated. By updating the model via inclusion of two CV datapoints at lower SVs (1500 V and 2000 V) accuracy was further improved to MAE ≤ 1.2 V. This improvement stems from the ability of the "guided" ML routine to accurately capture Type A and B behaviour, which was exhibited by only 2% and 17% of ions, respectively, within the dataset. Dispersion curve predictions of the database's most common Type C ions (81%) using the unguided and guided approaches exhibited average errors of 0.6 V and 0.1 V, respectively.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and WaterMine Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada and Bedrock Scientific Inc., Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada and WaterMine Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada and Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, 999077, Hong Kong
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26
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Naylor CN, Clowers BH. Reevaluating the Role of Polarizability in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:618-627. [PMID: 33533630 DOI: 10.1021/jasms.0c00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the expanding commercial availability of gas-phase separation systems that incorporate gas-phase mobility, there is a concurrent rise in efforts to cast the gas-phase mobility coefficient in terms of an ion-neutral collision cross-section (CCS). The motivating factors for this trend are varied, but many aim to complement experimental results with computationally generated CCS values from in silico structural approximations. Unfortunately, the current paradigm for relating experimental mobility results to computationally derived structures relies upon empirical approaches, including a myriad of variables that do not realistically bound the comparison. In this Critical Insight, we advocate for the development of a self-consistent experimental and computational framework that uses laboratory results to constrain the scope of the modeling effort. This paper aims to prompt discussion, challenge assumptions, and promote the development of more efficient, accurate computational techniques within the gas-phase ion measurement community. Specifically, we postulate whether experimental deviations from Langevin's polarization limit (Kpol) are suitable to estimate the relative contributions of hard-sphere collisions and long-range interactions within CCS values. Not surprisingly, different molecule classes exhibit different trends in the K/Kpol ratio when normalized for reduced mass, and the most common IMS calibrants (e.g., tune mix, polyalanine, tetraalkylammonium salts) follow different polarizability trends than many of the analytes probed in the literature. Succinctly, if gas-phase ion structure is largely invariant based upon the colliding neutral and newly developed experimental efforts can quantitatively capture ion polarizability, then modeling efforts describing a target analyte must be self-consistent as the collision neutral is changed in silico.
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Affiliation(s)
- Cameron N Naylor
- 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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