1
|
Roesch GC, Garand E. Tandem Mass-Selective Cryogenic Digital Ion Traps for Enhanced Cluster Formation. J Phys Chem A 2023; 127:7665-7672. [PMID: 37656038 DOI: 10.1021/acs.jpca.3c04706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
We present the implementation of tandem mass-selective cryogenic ion traps, designed to enhance the range of ion processing capabilities that can be performed prior to spectroscopic interrogation. We show that both the formation of ion clusters and mass filtering steps can be combined in a single cryogenic linear quadrupole ion trap driven by RF square waves. Mass filtering and mass isolation can be achieved by manipulation of the RF frequency and duty cycle. Very importantly, this scheme circumvents the need for high-amplitude RF voltages that can be incompatible with typical cryogenic ion processing conditions. In addition, proper adjustment of the stability boundaries during the clustering process allows for the preferential formation of a specific cluster size rather than a broad distribution of sizes. Lastly, we show that a specific cluster size can be formed, mass-selected, and then transferred to another ion trap for a second completely separate ion processing step. The instrumentation and modular design developed here expand the scope of ionic species and clusters that can be accessed by processing electrosprayed ions.
Collapse
Affiliation(s)
- Gina C Roesch
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| |
Collapse
|
2
|
Schultz M, Parker SL, Fernando MT, Wellalage MM, Thomas DA. Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:745-753. [PMID: 36975839 DOI: 10.1021/jasms.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transferring biomolecules from solution to vacuum facilitates a detailed analysis of molecular structure and dynamics by isolating molecules of interest from a complex environment. However, inherent in the ion desolvation process is the loss of solvent hydrogen bonding partners, which are critical for the stability of a condensed-phase structure. Thus, transfer of ions to vacuum can favor structural rearrangement, especially near solvent-accessible charge sites, which tend to adopt intramolecular hydrogen bonding motifs in the absence of solvent. Complexation of monoalkylammonium moieties (e.g., lysine side chains) with crown ethers such as 18-crown-6 can disfavor structural rearrangement of protonated sites, but no equivalent ligand has been investigated for deprotonated groups. Herein we describe diserinol isophthalamide (DIP), a novel reagent for the gas-phase complexation of anionic moieties within biomolecules. Complexation is observed to the C-terminus or side chains of the small model peptides GD, GE, GG, DF-OMe, VYV, YGGFL, and EYMPME in electrospray ionization mass spectrometry (ESI-MS) studies. In addition, complexation is observed with the phosphate and carboxylate moieities of phosphoserine and phosphotyrosine. DIP performs favorably in comparison to an existing anion recognition reagent, 1,1'-(1,2-phenylene)bis(3-phenylurea), that exhibits moderate carboxylate binding in organic solvent. This improved performance in ESI-MS experiments is attributed to reduced steric constraints to complexation with carboxylate groups of larger molecules. Overall, diserinol isophthalamide is an effective complexation reagent that can be applied in future work to study retention of solution-phase structure, investigate intrinsic molecular properties, and examine solvation effects.
Collapse
Affiliation(s)
- Madeline Schultz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Sarah L Parker
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Maleesha T Fernando
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Miyuru M Wellalage
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A Thomas
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Sherman SL, Fischer KC, Garand E. Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues. J Phys Chem A 2022; 126:4036-4045. [PMID: 35700447 DOI: 10.1021/acs.jpca.2c02584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR-IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. These observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.
Collapse
Affiliation(s)
- Summer L Sherman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kaitlyn C Fischer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
5
|
Sherman SL, Nickson KA, Garand E. Comment on "Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy". J Phys Chem Lett 2022; 13:2046-2050. [PMID: 35236072 DOI: 10.1021/acs.jpclett.1c02211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This Viewpoint presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev, et al. 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D2-tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Once these spectral effects are taken into account, we show that both clustering approaches yield similar cluster structures for the small GlyH+(H2O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298 K is explored using a series of model polyalanine chains.
Collapse
Affiliation(s)
- Summer L Sherman
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kathleen A Nickson
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
6
|
Saparbaev E, Yamaletdinov R, Boyarkin OV. Identification of Isomeric Lipids by UV Spectroscopy of Noncovalent Complexes with Aromatic Molecules. Anal Chem 2021; 93:12822-12826. [PMID: 34516082 DOI: 10.1021/acs.analchem.1c02866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The tremendous structural and isomeric diversity of lipids enables a wide range of their functions in nature but makes the identification of these biomolecules challenging. We distinguish and quantify isomeric lipids using cold ion UV fragmentation spectroscopy of their noncovalent complexes with aromatic amino acids and dipeptides. On the basis of structural simulations, specific isomer-sensitive aromatic "sensors" have been preselected for lipids of each studied class. Tyrosine appeared to be a good "sensor" to distinguish steroids and prostaglandins, which are rich in functional groups, while diphenylalanine is a better choice for sensing largely hydrophobic phospholipids. With this sensor, the relative concentrations of two isomeric glycerophospholipids mixed in solution have been determined with 3.3% accuracy, which should degrade only to 3.7% for a 14 s express measurement.
Collapse
Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry, Novosibirsk 630090, Russian Federation
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| |
Collapse
|
7
|
Affiliation(s)
- Martin Mayer
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
| | - Knut R. Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103 Leipzig, Germany
| |
Collapse
|
8
|
Saparbaev E, Aladinskaia V, Zviagin A, Boyarkin OV. Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy. J Phys Chem Lett 2021; 12:907-911. [PMID: 33439655 DOI: 10.1021/acs.jpclett.0c03678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The native-like structures of protonated glycine and peptide Gly3H+ were elucidated using cold ion IR spectroscopy of these biomolecules hydrated by a controlled number of water molecules. The complexes were generated directly from an aqueous solution using gentle electrospray ionization. Already with a single retained water molecule, GlyH+ exhibits the native-like structure characterized by a lack of intramolecular hydrogen bonds. We use our spectra to calibrate the available data for the same complexes, which are produced by cryogenic condensation of water onto the gas-phase glycine. In some conformers of these complexes, GlyH+ adopts the native-like structure, while in the others, it remains "kinetically" trapped in the intrinsic state. Upon condensation of 4-5 water molecules, the embedded amino acid fully adopts its native-like structure. Similarly, condensation of one water molecule onto the tripeptide is insufficient to fully eliminate its kinetically trapped intrinsic states.
Collapse
Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Viktoriia Aladinskaia
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| |
Collapse
|
9
|
Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
Collapse
Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
Collapse
Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| |
Collapse
|
11
|
Fischer KC, Sherman SL, Garand E. Competition between Solvation and Intramolecular Hydrogen-Bonding in Microsolvated Protonated Glycine and β-Alanine. J Phys Chem A 2020; 124:1593-1602. [DOI: 10.1021/acs.jpca.9b11977] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kaitlyn C. Fischer
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Summer L. Sherman
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
12
|
Zeng HJ, Yang N, Johnson MA. Introductory lecture: advances in ion spectroscopy: from astrophysics to biology. Faraday Discuss 2019; 217:8-33. [PMID: 31094388 DOI: 10.1039/c9fd00030e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This introduction provides a historical context for the development of ion spectroscopy over the past half century by following the evolution of experimental methods to the present state-of-the-art. Rather than attempt a comprehensive review, we focus on how early work on small ions, carried out with fluorescence, direct absorption, and photoelectron spectroscopy, evolved into powerful technologies that can now address complex chemical problems ranging from catalysis to biophysics. One of these developments is the incorporation of cooling and temperature control to enable the general application of "messenger tagging" vibrational spectroscopy, first carried out using ionized supersonic jets and then with buffer gas cooling in radiofrequency ion traps. Some key advances in the application of time-resolved pump-probe techniques to follow ultrafast dynamics are also discussed, as are significant benchmarks in the refinement of ion mobility to allow spectroscopic investigation of large biopolymers with well-defined shapes. We close with a few remarks on challenges and opportunities to explore molecular level mechanics that drive macroscopic behavior.
Collapse
Affiliation(s)
- Helen J Zeng
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA.
| | - Nan Yang
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA.
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
13
|
Fischer KC, Sherman SL, Voss JM, Zhou J, Garand E. Microsolvation Structures of Protonated Glycine and l-Alanine. J Phys Chem A 2019; 123:3355-3366. [DOI: 10.1021/acs.jpca.9b01578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kaitlyn C. Fischer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Summer L. Sherman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jonathan M. Voss
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jia Zhou
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|