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 (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.

Molecular Structures and Ion Mobility Cross Sections: Analysis of the Effects of He and N2 Buffer Gas.

An empirically observed correlation between ion mobility cross sections in helium and nitrogen buffer gases was examined as a function of temperature, molecular size, and shape. Experimental cross sections were determined for tetraglycine, bradykinin, angiotensin 2, melittin, and ubiquitin at 300 K and in the range from 80 to 550 K on home-built instruments and calculated by the projection superposition approximation (PSA) method. The PSA was also used to predict cross sections for larger systems such as human pancreatic alpha-amylase, concanavalin, Pichia pastoris lysyl oxidase, and Klebsiella pneumoniae acetolactate synthase. The data show that the ratio of cross sections in helium and nitrogen depends significantly on the temperature of the buffer gas as well as the size and shape of the analyte ion. Therefore, the analysis of the data indicates that a simple formula that seeks to quantitatively relate the momentum transfer cross sections observed in two distinct buffer gases lacks a sound physical basis.

Ion mobility analysis of molecular dynamics.

The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.

Factors contributing to the collision cross section of polyatomic ions in the kilodalton to gigadalton range: application to ion mobility measurements.

The projected superposition approximation (PSA) method was used to theoretically evaluate the factors contributing to the cross section measured in ion mobility experiments and to study how the significance of these factors varies with ion size from diglycine to a 1 µm oil droplet. Thousands of PSA calculations for ∼400 different molecules in the temperature range from 80 to 700 K revealed that the molecular framework made up of atomic hard spheres is, as expected, a major component of the cross section. However, the ion-buffer gas interaction is almost equally important for very small peptides, and although its significance decreases with increasing ion size, interaction is still a factor for megadalton ions. An additional major factor is the ion shape: Fully convex ions drifting in a buffer gas have a minimal frictional resisting force, whereas the resisting force increases with degree of ion surface concaveness. This added resistance is small for peptides and larger for proteins and increases the ion mobility cross section from 0 to greater than 40%. The proteins with the highest degree of concaveness reach a shape-effected friction similar to, and sometimes larger than that of, macroscopic particles such as oil droplets. In summary, our results suggest that the transition from nanoparticle (with Lennard-Jones-like interaction with the buffer gas) to macroscopic particle (with hard sphere-like interaction) occurs at ∼1 GDa.

Delivery of mobile dental services to dependent elderly people: results from a pilot study in rural Switzerland.

The objective of this pilot study was to provide data on the oral health status and oral health behaviour of care-dependent elderly people in the canton of Uri. The study aimed at assessing whether age and duration of living in a nursing home is associated with dental attendance, whether there is a relationship between age and the DMF-T index, and how high the risk was for participants to develop oral health problems. The study offered mobile dental services to people residing in nursing homes (NHG) and to community dwellers (CDG). Data was collected on demographics, medical history, presence of pain, ability to eat and oral health behaviour by means of a questionnaire. A clinical examination was performed and data on the oral status was collected. Statistical methods were: median tests, linear regressions and descriptive statistics. Uptake of the programme was low. 56 participants were examined. 47 participants (24 females, 23 males, average age 86.3 ± 7.36 years) resided in nursing home, nine participants (seven females, two males, average age 76 ± 12.8 years) were community dwellers. No significant differences were found between frequency of dental attendance and age (p = 0.35) or duration of stay in a nursing home (p = 0.55). The number of decayed teeth (p=0.005), missing teeth (p=0.01), and the DMF-T index (average in NHG = 26.5, CDG = 20.2, p < 0.001) increased, the number of filled teeth (p=0.02) decreased as age increased. Upon calculation of the 'Teamwerk-index', which takes into account oral health behaviour, dental caries, periodontal status, the majority of participants had a medium risk of developing oral health problems. Our pilot study in rural Switzerland provides first results of the oral health status in dependent elderly people. As people age, oral health deteriorates. More attention should be given in order to achieve better oral hygiene maintenance and more regular dental visits, to ensure a better oral health status in dependent elderly people.

Conformational stability of Syrian hamster prion protein PrP(90-231).

Many transmissible spongiform encephalopathies (TSEs) are believed to be caused by a misfolded form of the normal cellular prion protein (PrP(C)) known as PrP(Sc). While PrP(Sc) is known to be exceptionally stable and resistant to protease degradation, PrP(C) has not shown these same unusual characteristics. However, using ion mobility spectrometry mass spectrometry (IMS-MS), we found evidence for at least one very stable conformation of a truncated form of recombinant PrP(C) consisting of residues 90-231, which resists unfolding in the absence of solvent at high injection energies and at temperatures in excess of 600 K. We also report the first absolute collision cross sections measured for recombinant Syrian hamster prion protein PrP(90-231).

Hydration of protonated aromatic amino acids: phenylalanine, tryptophan, and tyrosine.

The first steps of hydration of the protonated aromatic amino acids phenylalanine, tryptophan, and tyrosine were studied experimentally employing a mass spectrometer equipped with a drift cell to examine the sequential addition of individual water molecules in equilibrium experiments and theoretically by a combination of molecular mechanics and electronic structure calculations (B3LYP/6-311++G**) on the three amino acid systems including up to five water molecules. It is found that both the ammonium and carboxyl groups offer good water binding sites with binding energies of the order of 13 kcal/mol for the first water molecule. Subsequent water molecules bind less strongly, in the range of 7-11 kcal/mol for the second through fifth water molecules. The ammonium group is able to host up to three water molecules and the carboxyl group one water molecule before additional water molecules bind either to the amino acid side chain as in tyrosine or to already-bound water in a second solvation shell around the ammonium group. Reasons for the surprisingly high water affinity of the neutral carboxyl group, comparable to that of the charge-carrying ammonium group, are found to be high intrinsic hydrophilicity, favorable charge-dipole alignment, and--for the case of multiply hydrated species--favorable dipole-dipole interaction among water molecules and the lack of alternative fully exposed hydration sites.

Protonated arginine and protonated lysine: hydration and its effect on the stability of salt-bridge structures.

Using a mass spectrometer equipped with a drift cell, water binding energies of protonated arginine (ArgH+) and protonated lysine (LysH+) were determined in equilibrium experiments and supplementary calculations at the B3LYP/6-311++G** level of theory. The binding energy of the first water molecule was measured to be 10.3 and 10.9 kcal/mol for ArgH+ and LysH+, respectively. Water binding energies decrease with increasing degree of hydration reaching values of 6-7 kcal/mol for the fourth and fifth water molecule. Theory reproduces this trend of decreasing binding energies correctly and theoretical water binding energies agree with experiment quantitatively within 2 kcal/mol. Lowest-energy theoretical structures of ArgH+ and LysH+ are characterized by protonated side chains and neutral alpha-amino and carboxyl groups which form intramolecular hydrogen bonds to the ionic group (charge solvation or CS structures). The salt bridge (SB) structures with two cationic groups (side chain and alpha-amine) and one anionic group (carboxyl) are 13.1 and 9.3 kcal/mol higher in energy for ArgH+ and LysH+, respectively. Theory indicated that the first water molecule binds to the ionic group of the CS structures of ArgH+ and LysH+. With increasing degree of hydration intramolecular interactions are replaced one by one with water bridges with water inserted into the intramolecular hydrogen bonds. Whereas the global minima of ArgH+.(H2O)n and LysH+.(H2O)n, n<7, were calculated to represent CS structures, 7-fold hydrated CS and SB structures, ArgH+.(H2O)7 and LysH+.(H2O)7, are nearly isoenergetic (within <1 kcal/mol).

Amyloid beta-protein: experiment and theory on the 21-30 fragment.

The structure of the 21-30 fragment of the amyloid beta-protein (Abeta) was investigated by ion mobility mass spectrometry and replica exchange dynamics simulations. Mutations associated with familial Alzheimer's disease (E22G, E22Q, E22K, and D23N) of Abeta(21-30) were also studied, in order to understand any structural changes that might occur with these substitutions. The structure of the WT peptide shows a bend and a perpendicular turn in the backbone which is maintained by a network of D23 hydrogen bonding. Results for the mutants show that substitutions at E22 do little to alter the overall structure of the fragment. A substitution at D23 resulted in a change of structure for Abeta(21-30). A comparison of these gas-phase studies to previous solution-phase studies reveals that the peptide can fold in the absence of solvent to a structure also seen in solution, highlighting the important role of the D23 hydrogen bonding network in stabilizing the fragment's folded structure.

Systematic study of the structures of potassiated tertiary amino acids: salt bridge structures dominate.

The gas-phase structures of a series of potassiated tertiary amino acids have been systematically investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, ion mobility spectrometry (IMS), and computational modeling. The examined analytes comprise a set of five linear N,N-dimethyl amino acids derived from N,N-dimethyl glycine and three cyclic N-methyl amino acids including N-methyl proline. The number of methylene groups in either the alkyl chain of the linear members or in the ring of the cyclic members of the series is gradually varied. The spectra of the cyclic potassiated molecular ions are similar and well resolved, whereas the clear signals in the respective spectra of the linear analytes increasingly overlap with longer alkyl chains. Measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311++G(2d,2p) level of theory to identify the structures present in the experimental studies. On the basis of these experiments and calculations, all potassiated molecular ions of this series adopt salt bridge structures in the gas phase, involving bidentate coordination of the potassium cation to the carboxylate moiety. The assigned salt bridge structures are predicted to be the global minima on the potential energy surfaces. IMS cross-section measurements of the potassiated systems show a monotonic increase with growing system size, suggesting that the precursor ions adopt the same type of structure and comparisons between experimental and theoretical cross sections are consistent with salt bridge structures and the IRMPD results.

Interactions of the hormone oxytocin with divalent metal ions.

The interaction of the cyclic nonapeptide oxytocin (OT) with a number of alkaline earth and divalent transition metal ions (X(2+)) was examined employing mass spectrometry (MS) and ion mobility spectrometry (IMS) techniques in combination with molecular dynamics (MD) and density functional theory (DFT) calculations. Under acidic conditions it was found that OT exhibits an exceptionally strong affinity for all divalent metal ions resulting in strong [OT + X](2+) peaks in the mass spectrum. Under basic conditions only Cu(2+) and Ni(2+)-OT complexes were detected and these were singly, doubly, triply, or quadruply deprotonated. Collision-induced dissociation of the [OT - 3H + Cu](-) complex yielded exclusively C-terminal Cu(2+)-containing fragments (Cu(2+)fragment(3-)), suggesting that the Cu(2+) ligation site includes deprotonated C-terminal backbone amide nitrogen atoms and the N-terminal amino nitrogen atom in [OT - 3H + Cu](-). MD and DFT calculations indicate a square-planar complex is consistent with these observations and with experimental collision cross sections. MD and DFT calculations also indicate either an octahedral or trigonal-bipyramidal complex between Zn(2+) and OT is lowest in energy with carbonyl oxygens being the primary ligation sites. Both complexes yield cross sections in agreement with experiment. The biological impact of the structural changes induced in OT by divalent metal ion coodination is discussed.

Spermine binding to Parkinson's protein alpha-synuclein and its disease-related A30P and A53T mutants.

Aggregation of alpha-synuclein (alpha-syn), a protein implicated in Parkinson's disease (PD), is believed to progress through formation of a partially folded intermediate. Using nanoelectrospray ionization (nano-ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for alpha-syn and its disease-related A53T mutant with net charges of -6, -7, and -8. For the other early onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of -6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of -10 to a net charge of -6. This charge reduction is accompanied by a dramatic size reduction of about a factor of 2 (cross section of 2600 A2 (-10 charge state) down to 1430 A2 (-6 charge state)). We conclude that spermine increases the aggregation rate of alpha-syn by inducing a collapsed conformation, which then proceeds to form aggregates.

Amyloid beta-protein monomer structure: a computational and experimental study.

The structural properties of the Abeta42 peptide, a main constituent of the amyloid plaques formed in Alzheimer's disease, were investigated through a combination of ion-mobility mass spectrometry and theoretical modeling. Replica exchange molecular dynamics simulations using a fully atomic description of the peptide and implicit water solvent were performed on the -3 charge state of the peptide, its preferred state under experimental conditions. Equilibrated structures at 300 K were clustered into three distinct families with similar structural features within a family and with significant root mean square deviations between families. An analysis of secondary structure indicates the Abeta42 peptide conformations are dominated by loops and turns but show some helical structure in the C-terminal hydrophobic tail. A second calculation on Abeta42 in a solvent-free environment yields compact structures turned "inside out" from the solution structures (hydrophobic parts on the outside, polar parts on the inside). Ion mobility experiments on the Abeta42 -3 charge state electrosprayed from solution yield a bimodal arrival time distribution. This distribution can be quantitatively fit using cross-sections from dehydrated forms of the three families of calculated solution structures and the calculated solvent-free family of structures. Implications of the calculations on the early stages of aggregation of Abeta42 are discussed.

Structure of the 21-30 fragment of amyloid beta-protein.

Folding and self-assembly of the 42-residue amyloid beta-protein (Abeta) are linked to Alzheimer's disease (AD). The 21-30 region of Abeta, Abeta(21-30), is resistant to proteolysis and is believed to nucleate the folding of full-length Abeta. The conformational space accessible to the Abeta(21-30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the "native" state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24-K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non-native states of this peptide are compact and retain a native-like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures.

Alpha-synuclein: stable compact and extended monomeric structures and pH dependence of dimer formation.

The protein alpha-synuclein, implicated in Parkinson's disease, was studied by combining nano-electrospray ionization (N-ESI) mass spectrometry and ion mobility. It was found that both the charge-state distribution in the mass spectra and the average protein shape deduced from ion mobility data, depend on the pH of the spray solution. Negative-ion N-ESI of pH 7 solutions yielded a broad charge-state distribution from -6 to -16, centered at -11, and ion mobility data consistent with extended protein structures. Data obtained for pH 2.5 solutions, on the other hand, showed a narrow charge-state distribution from -6 to -11, centered at -8, and ion mobilities in agreement with compact alpha-synuclein structures. The data indicated that there are two distinct families of structures: one consisting of relatively compact proteins with eight or less negative charges and one consisting of relatively extended structures with nine or more charges. The average cross section of a-synuclein at pH 2.5 is 33% smaller than for the extended protein sprayed from pH 7 solution. Significant dimer formation was observed when sprayed from pH 7 solution but no dimers were observed from the low pH solution. A plausible mechanism for aggregate formation in solution is proposed.

Structural stability from solution to the gas phase: native solution structure of ubiquitin survives analysis in a solvent-free ion mobility-mass spectrometry environment.

The conformations of desolvated ubiquitin ions, lifted into the gas phase by electrospray ionization (ESI), were characterized by ion mobility spectrometry (IMS) and compared to the solution structures they originated from. The IMS instrument combining a two-meter helium drift tube with a quadrupole time-of-flight mass spectrometer was built in-house. Solutions stabilizing the native state of ubiquitin yielded essentially one family of tightly folded desolvated ubiquitin structures with a cross section matching the size of the native state (1000 Å(2)). Solutions favoring the A state yielded several well-defined families of significantly unfolded conformations (1800-2000 Å(2)) matching in size conformations between the A state and a fully unfolded state. On the basis of these results and a wealth of data available in the literature, we conclude that the native state of ubiquitin is preserved in the transition from solution to the desolvated state during the ESI process and survives for >100 ms in a 294 K solvent-free environment. The A state, however, is charged more extensively than the native state during ESI and decays more rapidly following ESI. A state ions unfold on a time scale equal to or shorter than the experiment (≤50 ms) to more extended structures.

Ion mobility-mass spectrometry reveals a conformational conversion from random assembly to ß-sheet in amyloid fibril formation.

Amyloid cascades that lead to peptide ß-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with cellular machinery. The location and cause of the transformation from a natively unstructured assembly to the ß-sheet oligomers found in all fibrils is important in understanding disease onset and the development of therapeutic agents. Largely, research on this early oligomeric region was unsuccessful because all the traditional techniques measure only the average oligomer properties of the ensemble. We utilized ion-mobility methods to deduce the peptide self-assembly mechanism and examined a series of amyloid-forming peptides clipped from larger peptides or proteins associated with disease. We provide unambiguous evidence for structural transitions in each of these fibril-forming peptide systems and establish the potential of this method for the development of therapeutic agents and drug evaluation.

The effect of calcium ions and peptide ligands on the relative stabilities of the calmodulin dumbbell and compact structures.

A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Ca(n)(2+)-CaM complexes were observed in calcium-containing solutions, n = 0-4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n = 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII(290-309), the CaM target domain of the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca(4)(2+)-CaM-CaMKII(290-309) complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM-peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM-peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.

Structural analysis of prion proteins by means of drift cell and traveling wave ion mobility mass spectrometry.

The prion protein (PrP) is implicitly involved in the pathogenesis of transmissible spongiform encephalopathies (TSEs). The conversion of normal cellular PrP (PrP(C)), a protein that is predominantly alpha-helical, to a beta-sheet-rich isoform (PrP(Sc)), which has a propensity to aggregate, is the key molecular event in prion diseases. During its short life span, PrP can experience two different pH environments; a mildly acidic environment, whilst cycling within the cell, and a neutral pH when it is glycosyl phosphatidylinositol (GPI)-anchored to the cell membrane. Ion mobility (IM) combined with mass spectrometry has been employed to differentiate between two conformational isoforms of recombinant Syrian hamster prion protein (SHaPrP). The recombinant proteins studied were alpha-helical SHaPrP(90-231) and beta-sheet-rich SHaPrP(90-231) at pH 5.5 and pH 7.0. The recombinant proteins have the same nominal mass-to-charge ratio (m/z) but differ in their secondary and tertiary structures. A comparison of traveling-wave (T-Wave) ion mobility and drift cell ion mobility (DCIM) mass spectrometry estimated and absolute cross-sections showed an excellent agreement between the two techniques. The use of T-Wave ion mobility as a shape-selective separation technique enabled differentiation between the estimated cross-sections and arrival time distributions (ATDs) of alpha-helical SHaPrP(90-231) and beta-sheet-rich SHaPrP(90-231) at pH 5.5. No differences in cross-section or ATD profiles were observed between the protein isoforms at pH 7.0. The findings have potential implications for a new ante-mortem screening assay, in bodily fluids, for prion misfolding diseases such as TSEs.

Amyloid-ß protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease.

In recent years, small protein oligomers have been implicated in the aetiology of a number of important amyloid diseases, such as type 2 diabetes, Parkinson's disease and Alzheimer's disease. As a consequence, research efforts are being directed away from traditional targets, such as amyloid plaques, and towards characterization of early oligomer states. Here we present a new analysis method, ion mobility coupled with mass spectrometry, for this challenging problem, which allows determination of in vitro oligomer distributions and the qualitative structure of each of the aggregates. We applied these methods to a number of the amyloid-ß protein isoforms of Aß40 and Aß42 and showed that their oligomer-size distributions are very different. Our results are consistent with previous observations that Aß40 and Aß42 self-assemble via different pathways and provide a candidate in the Aß42 dodecamer for the primary toxic species in Alzheimer's disease.