Ion Mobility Mass Spectrometry Measurements Research Articles

Interfacial Dimerization by Organic Radical Reactions during Heterogeneous Oxidative Aging of Oxygenated Organic Aerosols.

Oxidative aging of atmospheric organic aerosols (OA) substantially modifies their chemical compositions, physical properties, and hence the various environmental impacts. Here, we report observations of a previously unrecognized process leading to dimer formation during heterogeneous •OH-initiated oxidative aging of oxygenated OA. Isomer-resolved ion mobility mass spectrometry measurements and reaction-diffusion kinetic simulations are in good agreement, elucidating new mechanisms of dimerization by organic radical (i.e., peroxy and alkoxy radicals) cross reactions using glutaric acid as a surrogate oxygenated OA. These radical reactions are predicted to occur more prominently near the gas-particle interface following oxidation, especially in diffusion-limited viscous OA particles. Chemical structure analysis shows that esters dominate the detected dimers, followed by organic peroxides and ethers, highlighting the importance of acyl peroxy and acyloxy radicals. Simulations suggest that the reported dimer formation through the new interfacial mechanism could be appreciable under both laboratory and ambient conditions. Therefore, the dimers that are formed and enriched at the gas-particle interface are expected to play a crucial role in the effective reactivity, volatility, viscosity, and hygroscopicity of aged OA particles.

Recommendations for reporting ion mobility Mass Spectrometry measurements.

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K 0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method‐dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Ion Mobility-Mass Spectrometry Reveals a Dipeptide That Acts as a Molecular Chaperone for Amyloid β.

Previously, we discovered and structurally characterized a complex between amyloid β 1-40 and the neuropeptide leucine enkephalin. This work identified leucine enkephalin as a potentially useful starting point for the discovery of peptide-related biotherapeutics for Alzheimer's disease. In order to better understand such complexes that are formed in vitro, we describe here the analysis of a series of site-directed amino acid substitution variants of both peptides, covering the leucine enkephalin sequence in its entirety and a large number of selected residues of amyloid β 1-40 (residues: D1, E3, F4, R5, H6, Y10, E11, H13, H14, Q15, K16, E22, K28, and V40). Ion mobility-mass spectrometry measurements and molecular dynamics simulations reveal that the hydrophobic C-terminus of leucine enkephalin (Phe-Leu, FL) is crucial for the formation of peptide complexes. As such, we explore here the interaction of the dipeptide FL with both wildtype and variant forms of amyloid β in order to structurally characterize the complexes formed. We find that FL binds preferentially to amyloid β oligomers and attaches to amyloid β within the region between its N-terminus and its hydrophobic core, most specifically at residues Y10 and Q15. We further show that FL is able to prevent fibril formation.

Ion Mobility-Mass Spectrometry Analysis of Cross-Linked Intact Multiprotein Complexes: Enhanced Gas-Phase Stabilities and Altered Dissociation Pathways.

Analysis of protein complexes by ion mobility-mass spectrometry is a valuable method for the rapid assessment of complex composition, binding stoichiometries, and structures. However, capturing labile, unknown protein assemblies directly from cells remains a challenge for the technology. Furthermore, ion mobility-mass spectrometry measurements of complexes, subcomplexes, and subunits are necessary to build complete models of intact assemblies, and such data can be difficult to acquire in a comprehensive fashion. Here, we present the use of novel mass spectrometry cleavable cross-linkers and tags to stabilize intact protein complexes for ion mobility-mass spectrometry. Our data reveal that tags and linkers bearing permanent charges are superior stabilizers relative to neutral cross-linkers, especially in the context of retaining compact forms of the assembly under a wide array of activating conditions. In addition, when cross-linked protein complexes are collisionally activated in the gas phase, a larger proportion of the product ions produced are often more compact and reflect native protein subcomplexes when compared with unmodified complexes activated in the same fashion, greatly enabling applications in structural biology.

Evaluation of Ion Mobility-Mass Spectrometry for Comparative Analysis of Monoclonal Antibodies.

Analytical techniques capable of detecting changes in structure are necessary to monitor the quality of monoclonal antibody drug products. Ion mobility mass spectrometry offers an advanced mode of characterization of protein higher order structure. In this work, we evaluated the reproducibility of ion mobility mass spectrometry measurements and mobiligrams, as well as the suitability of this approach to differentiate between and/or characterize different monoclonal antibody drug products. Four mobiligram-derived metrics were identified to be reproducible across a multi-day window of analysis. These metrics were further applied to comparative studies of monoclonal antibody drug products representing different IgG subclasses, manufacturers, and lots. These comparisons resulted in some differences, based on the four metrics derived from ion mobility mass spectrometry mobiligrams. The use of collision-induced unfolding resulted in more observed differences. Use of summed charge state datasets and the analysis of metrics beyond drift time allowed for a more comprehensive comparative study between different monoclonal antibody drug products. Ion mobility mass spectrometry enabled detection of differences between monoclonal antibodies with the same target protein but different production techniques, as well as products with different targets. These differences were not always detectable by traditional collision cross section studies. Ion mobility mass spectrometry, and the added separation capability of collision-induced unfolding, was highly reproducible and remains a promising technique for advanced analytical characterization of protein therapeutics. Graphical Abstract ᅟ.

Differentiation of prototropic ions in regioisomeric caffeoyl quinic acids by electrospray ion mobility mass spectrometry.

A series of dietary important regioisomeric chlorogenic acids were investigated by ion mobility mass spectrometry (IM-MS). The existence of prototropic isomers separated in the drift dimension was observed and investigated further using tandem mass spectrometry (MS/MS) and compared with suitable synthetic analogues. Using a quadrupole ion mobility time-of-flight mass spectrometer, the IM-MS and IM-MS/MS spectra of selected chlorogenic acids were recorded in the negative ion mode and compared with synthetic analogues. Regioisomeric di- and monocaffeoyl quinic acids can be readily separated and investigated using IM-MS. Comparison of drift times allows assignment of the regiochemistry of precursor ions as well as for fragment ions. For 5-caffeoyl quinic acid the existence of prototropic ions was suggested and probed using synthetic analogues, unable to show this type of isomerism. These investigations suggest the presence of prototropic isomers with carboxylate and phenolate sites, respectively. We report on IM-MS measurements on regioisomeric mono- and dicaffeoyl quinic acids, which are important dietary natural products. Both classes of compounds can be readily separated by IM-MS in the drift time dimension and, following MS(2) experiments, fragment ion regiochemistry unambiguously determined. 5-Caffeoyl quinic acid shows two IM-MS signals, which we assign to prototropic isomers after comparison with suitable synthetic analogues, with a negative charge located at the carboxalate or phenolate functionality, respectively.

Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements.

Applying Hadamard transform multiplexing to ion mobility separations (IMS) can significantly improve the signal-to-noise ratio and throughput for IMS coupled mass spectrometry (MS) measurements by increasing the ion utilization efficiency. However, it has been determined that fluctuations in ion intensity as well as spatial shifts in the multiplexed data lower the signal-to-noise ratios and appear as noise in downstream processing of the data. To address this problem, we have developed a novel algorithm that discovers and eliminates data artifacts. The algorithm employs an analytical approach to identify and remove artifacts from the data, decreasing the likelihood of false identifications in subsequent data processing. Following application of the algorithm, IMS-MS measurement sensitivity is greatly increased and artifacts that previously limited the utility of applying the Hadamard transform to IMS are avoided. Figure ᅟ

Conformational Ordering of Biomolecules in the Gas Phase: Nitrogen Collision Cross Sections Measured on a Prototype High Resolution Drift Tube Ion Mobility-Mass Spectrometer

Ion mobility-mass spectrometry measurements which describe the gas-phase scaling of molecular size and mass are of both fundamental and pragmatic utility. Fundamentally, such measurements expand our understanding of intrinsic intramolecular folding forces in the absence of solvent. Practically, reproducible transport properties, such as gas-phase collision cross-section (CCS), are analytically useful metrics for identification and characterization purposes. Here, we report 594 CCS values obtained in nitrogen drift gas on an electrostatic drift tube ion mobility-mass spectrometry (IM-MS) instrument. The instrument platform is a newly developed prototype incorporating a uniform-field drift tube bracketed by electrodynamic ion funnels and coupled to a high resolution quadrupole time-of-flight mass spectrometer. The CCS values reported here are of high experimental precision (±0.5% or better) and represent four chemically distinct classes of molecules (quaternary ammonium salts, lipids, peptides, and carbohydrates), which enables structural comparisons to be made between molecules of different chemical compositions for the rapid “omni-omic” characterization of complex biological samples. Comparisons made between helium and nitrogen-derived CCS measurements demonstrate that nitrogen CCS values are systematically larger than helium values; however, general separation trends between chemical classes are retained regardless of the drift gas. These results underscore that, for the highest CCS accuracy, care must be exercised when utilizing helium-derived CCS values to calibrate measurements obtained in nitrogen, as is the common practice in the field.

Alkali Metal Cation-Induced Destabilization of Gas-Phase Protein–Ligand Complexes: Consequences and Prevention

Electrospray ionization, now a well established technique for studying noncovalent protein-ligand interactions, is prone to production of alkali metal adducts. Here it is shown that this adduction significantly destabilizes the interactions between two model proteins and their ligands and that destabilization correlates with cation size. For both the [FKBP·FK506] and [lysozyme·NAG(n)] systems, dissociation of the metalated complex occurs at markedly lower collision energies than their purely protonated equivalents. Dependency upon size of the metal(+) demonstrates the importance of electrostatic charge density during the dissociation process. Differences in the gas phase basicities (GBapp) of the multiply charged protein ions and proton and sodium affinities of the ligands explain the observed charge partitioning during dissociation of the complexes. Ion mobility-mass spectrometry measurements demonstrate that metal cation adduction does not induce a significant increase in unfolding of the polypeptides, indicating that this is not the principal mechanism responsible for destabilization. Destabilizing effects can be largely reduced by exposing the electrospray to solvent (e.g., acetonitrile) vapor, a method that acts to reduce the amount of adduct formation as well as decrease the charge states of the resulting ions. This approach leads to more accurate determination of apparent K(D)s in the presence of trace alkali metals.

Ion Mobility-Mass Spectrometry Measurements Combined with Molecular Modeling Yields the Architecture of DNA Polymerase Complexes

Understanding how DNA polymerases interact with the rest of the replication machinery is of primary importance in unraveling some long-standing questions surrounding the mechanisms of DNA replication. We have been developing a method that combines both molecular and coarse-grained modeling and ion mobility-mass spectrometry (IM-MS) measurements in order to determine the positions of the protein subunits within the complex. The method works by first ionizing and desolvating the protein assemblies using nano-electrospray ionization. We then estimate the sizes of the protein ions by measuring their transit time through an IM separator, and measure their masses to determine their composition. To construct a model of the complex, MS information is used to infer subunit connectivity and IM information is used to filter the size of the assembly against a field of computationally derived model structures. Central to our method is the use of these measurements on various subcomplexes generated either in the solution or gas phases. When available, we use crystal structures of proteins and subcomplexes to build up models of complexes of unknown architecture, calculating and comparing their sizes with what is being measured by IM. Here, we present our most recent models for three different polymerases (II, III, and IV) bound to the prokaryotic DNA sliding clamp, the clamp loader bound to the clamp, and the chi-psi dimer bound to the clamp loader. The presentation will be evenly balanced between the development of this hybrid approach and its application to DNA polymerase III.

Collisional Activation of Protein Complexes: Picking Up the Pieces

Mass spectrometry is fast becoming a vital approach not only for the identification and quantification of proteins, but also for the study of the noncovalent assemblies they form. Approaches for ionizing, transmitting, and detecting protein complexes intact in the mass spectrometer are now well established. The challenge has therefore shifted to developing and applying mass spectrometry approaches to elucidate the structure of such species. A crucial aspect to this goal is inducing their disassembly in the gas phase to mine information as to their composition and organization. Here the consequences of collisionally activating protein complexes are illustrated through ion mobility mass spectrometry measurements and discussed in the context of the current literature. Although a consensus view of the mechanism of dissociation is starting to emerge, it is also clear that a number of aspects remain unresolved. These outstanding questions and frontier challenges must be addressed if gas-phase dissociative approaches are to reach their full potential in the study of protein assemblies.