Recommendations for reporting ion mobility mass spectrometry measurements

© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. 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 (K0) 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

Deciphering the Specific High-Affinity Binding of Cucurbit[7]uril to Amino Acids in Water

This work presents a systematic study on the host–guest interactions between the macrocyclic host molecule cucurbit[7]­uril (CB[7]) and amino acids (AAs) including three basic AAs (Lys, Arg, and His) and three aromatic AAs (Phe, Tyr, and Trp) to elucidate the origin of the high selectivity of CB[7] toward AA residues in proteins. Complex formation between CB[7] and each AA was examined in solution (by isothermal titration calorimetry and NMR) as well as in the gas phase (by ion mobility mass spectrometry and collision-induced dissociation), and the results were further combined with computational investigations. Generally, the aromatic AAs show higher binding affinities than the basic AAs in buffer solutions with various pH values. On the contrary, the gas-phase stabilities of the basic AA complex ions are higher than those of the aromatic AA complex ions, suggesting that the direct ion–dipole interactions between the charged side chains of the basic AAs and the polar carbonyl groups of CB[7] predominate in the absence of water. The ion–dipole interactions are less significant in water, since the original interactions of the guests with water are lost upon complex formation. In contrast, the transfer of the hydrophobic groups from the bulk into the hydrophobic CB[7] cavity suffers less from the desolvation penalty, resulting in higher binding affinities in water. Therefore, initial guest solvation is another key factor which should be considered when designing high-affinity host–guest systems, in addition to the contribution from the release of high-energy water molecules from the CB[7] cavity (<i>J. Am. Chem. Soc.</i> <b>2012</b>, <i>134</i>, 15318–15323)

Host–Guest Chemistry in the Gas Phase: Complex Formation with 18-Crown-6 Enhances Helicity of Alanine-Based Peptides

The gas-phase helix propensities of alanine-based polypeptides are studied with different locations of a Lys residue and host–guest interactions with 18-Crown-6 (18C6). A series of model peptides Ac-Ala_9–<i>n</i>-LysH⁺-Ala_<i>n</i> (<i>n</i> = 0, 1, 3, 5, 7, and 9) is examined alone and with 18C6 using traveling wave ion mobility mass spectrometry combined with molecular dynamics (MD) simulations. The gas-phase helices are observed from the peptides whose Lys residue is located close to the C-terminus so that the Lys exerts its capping effect on the C-terminal carbonyl groups. The peptides, which interact with 18C6 in the gas phase, show enhanced helical propensities. The enhanced helicity of the peptide in the complex is attributed by isolation of the Lys butylammonium group from the helix backbone and the interaction of methylene groups of 18C6, which possess localized positive partial charges, with C-terminal carbonyl groups serving as a cap to stabilize the helix

Molecular Insights into Human Serum Albumin as a Receptor of Amyloid-β in the Extracellular Region

Regulation of amyloid-β (Aβ) aggregation by metal ions and proteins is essential for understanding the pathology of Alzheimer’s disease (AD). Human serum albumin (HSA), a regulator of metal and protein transportation, can modulate metal–Aβ interactions and Aβ aggregation in human fluid; however, the molecular mechanisms for such activities remain unclear. Herein, we report the molecular-level complexation between Zn­(II), Cu­(II), Aβ, and HSA, which is able to alter the aggregation and cytotoxicity of Aβ peptides and induce their cellular transportation. In addition, a single Aβ monomer-bound HSA is observed with the structural change of Aβ from a random coil to an α-helix. Small-angle X-ray scattering (SAXS) studies indicate that Aβ–HSA complexation causes no structural variation of HSA in solution. Conversely, ion mobility mass spectrometry (IM-MS) results present that Aβ prevents the shrinkage of the V-shaped groove of HSA in the gas phase. Consequently, for the first time, HSA is demonstrated to predominantly capture a single Aβ monomer at the groove using the phase transfer of a protein heterodimer from solution to the gas phase. Moreover, HSA sequesters Zn­(II) and Cu­(II) from Aβ while maintaining Aβ–HSA interaction. Therefore, HSA is capable of controlling metal-free and metal-bound Aβ aggregation and aiding the cellular transportation of Aβ via Aβ–HSA complexation. The overall results and observations regarding HSA, Aβ, and metal ions advance our knowledge of how protein–protein interactions associated with Aβ and metal ions could be linked to AD pathogenesis

Elucidating Molecular Structures of Nonalkylated and Short-Chain Alkyl (<i>n</i> < 5, (CH₂)_<i>n</i>) Aromatic Compounds in Crude Oils by a Combination of Ion Mobility and Ultrahigh-Resolution Mass Spectrometries and Theoretical Collisional Cross-Section Calculations

Ultrahigh-resolution mass spectrometry has allowed the determination of elemental formulas of the compounds comprising crude oils. However, elucidating molecular structures remains an analytical challenge. Herein, we propose and demonstrate an approach combining ion mobility mass spectrometry (IM-MS), ultrahigh-resolution mass spectrometry, and theoretical collisional cross-section (CCS) calculations to determine the molecular structures of aromatic compounds found in crude oils. The approach is composed of three steps. First, chemical structures are suggested based on the elemental formulas determined from ultrahigh-resolution mass spectra. Second, theoretical CCS values are calculated based on these proposed structures. Third, the calculated CCS values of the proposed structures are compared with experimentally determined CCS values from IM-MS data to provide proposed structures. For proof of concept, 31 nonalkylated and short-chain alkyl (<i>n</i> < 5, (CH₂)_<i>n</i>) aromatic compounds commonly observed in crude oils were analyzed. Theoretical and experimental CCS values matched within a 5% RMS error. This approach was then used to propose structures of compounds in selected <i>m</i>/<i>z</i> regions of crude oil samples. Overall, the combination of ion mobility mass spectrometry, ultrahigh-resolution mass spectrometry, and theoretical calculations was shown to be a useful tool for elucidating chemical structures of compounds in complex mixtures

Probing Distinct Fullerene Formation Processes from Carbon Precursors of Different Sizes and Structures

Fullerenes, cage-structured carbon allotropes, have been the subject of extensive research as new materials for diverse purposes. Yet, their formation process is still not clearly understood at the molecular level. In this study, we performed laser desorption ionization-ion mobility-mass spectrometry (LDI-IM-MS) of carbon substrates possessing different molecular sizes and structures to understand the formation process of fullerene. Our observations show that the formation process is strongly dependent on the size of the precursor used, with small precursors yielding small fullerenes and large graphitic precursors generally yielding larger fullerenes. These results clearly demonstrate that fullerene formation can proceed via both bottom-up and top-down processes, with the latter being favored for large precursors and more efficient at forming fullerenes. Furthermore, we observed that specific structures of carbon precursors could additionally affect the relative abundance of C₆₀ fullerene. Overall, this study provides an advanced understanding of the mechanistic details underlying the formation processes of fullerene

Host–Guest Chemistry from Solution to the Gas Phase: An Essential Role of Direct Interaction with Water for High-Affinity Binding of Cucurbit[<i>n</i>]urils

An investigation of the host–guest chemistry of cucurbit­[<i>n</i>]­uril (CB­[<i>n</i>], <i>n</i> = 6 and 7) with α,ω-alkyldiammonium guests (H₂N­(CH₂)_<i>x</i>NH₂, <i>x</i> = 4, 6, 8, 10, and 12) both in solution and in the gas phase elucidates their intrinsic host–guest properties and the contribution of solvent water. Isothermal titration calorimetry and nuclear magnetic resonance measurements indicate that all alkyldiammonium cations have inclusion interactions with CB­[<i>n</i>] except for the CB[7]–tetramethylenediamine complex in aqueous solution. The electrospray ionization of mixtures of CB­[<i>n</i>] and the alkyldiammonium guests reflects their solution phase binding constants. Low-energy collision-induced dissociations indicate that, after the transfer of the CB­[<i>n</i>]–alkyldiammonium complex to the gas phase, its stability is no longer correlated with the binding properties in solution. Gas phase structures obtained from density functional theory calculations, which support the results from the ion mobility measurements, and molecular dynamics simulated structures in water provide a detailed understanding of the solvated complexes. In the gas phase, the binding properties of complexation mostly depend on the ion–dipole interactions. However, the ion–dipole integrity is strongly affected by hydrogen bonding with water molecules in the aqueous condition. Upon the inclusion of water molecules, the intrinsic characteristics of the host–guest binding are dominated by entropic-driven thermodynamics

Probing Conformational Change of Intrinsically Disordered α‑Synuclein to Helical Structures by Distinctive Regional Interactions with Lipid Membranes

α-Synuclein (α-Syn) is an intrinsically disordered protein, whose fibrillar aggregates are associated with the pathogenesis of Parkinson’s disease. α-Syn associates with lipid membranes and forms helical structures upon membrane binding. In this study, we explored the helix formation of α-Syn in solution containing trifluoroethanol using small-angle X-ray scattering and electrospray ionization ion mobility mass spectrometry. We then investigated the structural transitions of α-Syn to helical structures via association with large unilamellar vesicles as model lipid membrane systems. Hydrogen–deuterium exchange combined with electrospray ionization mass spectrometry was further utilized to understand the details of the regional interaction mechanisms of α-Syn with lipid vesicles based on the polarity of the lipid head groups. The characteristics of the helical structures were observed with α-Syn by adsorption onto the anionic phospholipid vesicles via electrostatic interactions between the N-terminal region of the protein and the anionic head groups of the lipids. α-Syn also associates with zwitterionic lipid vesicles and forms helical structures via hydrophobic interactions. These experimental observations provide an improved understanding of the distinct structural change mechanisms of α-Syn that originate from different regional interactions of the protein with lipid membranes and subsequently provide implications regarding diverse protein–membrane interactions related to their fibrillation kinetics