Ion Mobility Mass Spectrometry Unveils Global Protein Conformations in Response to Conditions that Promote and Reverse Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) is a process by which biomacromolecules, particularly proteins, condense into a dense phase that resembles liquid droplets. Dysregulation of LLPS is implicated in disease, yet the relationship between protein conformational changes and LLPS remains difficult to discern. This is due to the high flexibility and disordered nature of many proteins that phase separate under physiological conditions and their tendency to oligomerize. Here, we demonstrate that ion mobility mass spectrometry (IM-MS) overcomes these limitations. We used IM-MS to investigate the conformational states of full-length ubiquilin-2 (UBQLN2) protein, LLPS of which is driven by high-salt concentration and reversed by noncovalent interactions with ubiquitin (Ub). IM-MS revealed that UBQLN2 exists as a mixture of monomers and dimers and that increasing salt concentration causes the UBQLN2 dimers to undergo a subtle shift toward extended conformations. UBQLN2 binds to Ub in 2:1 and 2:2 UBQLN2/Ub complexes, which have compact geometries compared to free UBQLN2 dimers. Together, these results suggest that extended conformations of UBQLN2 are correlated with UBQLN2's ability to phase separate. Overall, delineating protein conformations that are implicit in LLPS will greatly increase understanding of the phase separation process, both in normal cell physiology and disease states.

Energy-Resolved Ion Mobility Spectrometry: Composite Breakdown Curves for Distinguishing Isomeric Product Ions.

Identification of lipopeptides (LpAA) synthesized from bacteria involves the study of structural characterization. Twenty LpAA have been characterized using commercial tandem high-resolution mass spectrometers in negative electrospray, employing nonresonant excitation in "RF only" collision cells and generally behave identically. However, [LpAA-H]- (AA = Asp or Glu) shows surprising fragmentation pathways, yielding a complementary fatty acid carboxylate and dehydrated amino acid fragment anions. In this study, the dissociation mechanisms of [C12Glu-H]- were determinate using energy-resolved mass spectrometry (ERMS). Product ion breakdown profiles are, generally, unimodal with full width at half-maximum (fwhm) increasing as product ion m/z ratios decrease, except for the two product ions of interest (fatty acid carboxylate and dehydrated glutamate) characterized by broad and composite profiles. Such behavior was already shown for other ions using a custom-built guided ion beam mass spectrometer. In this study, we investigate the meaning of these particular profiles from an ERMS breakdown, using fragmentation mechanisms depending on the collision energy. ERMS on line with ion mobility spectrometry (IMS), here called ER-IMS, provides a way to probe such questions. Broad or composite profiles imply that the corresponding product ions may be generated by two (or more) pathways, resulting in common or isomeric product ion structures. ER-IMS analysis indicates that the fatty acid carboxylate product ion is produced with a common structure through different pathways, while dehydrated glutamate has two isomeric forms depending on the mechanism involved. Drift time values correlate with the calculated collision cross section that confirms the product ion structures and fragmentation mechanisms.

Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry.

The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.

Mapping Isomeric Peptides Derived from Biopharmaceuticals Using High-Resolution Ion Mobility Mass Spectrometry.

The identification and localization of isomeric peptide modifications is a critical requirement of the biopharmaceutical industry. Despite the ability of liquid chromatography-mass spectrometry to identify many of the common post translational modifications, the identification of isobaric or racemized peptides is confounded by modern mass spectrometry-based techniques. Here, we present a novel approach combining liquid chromatography with a high-resolution ion mobility mass spectrometry system to differentiate peptide and peptide fragments based upon their mobility and mass.

Investigations into pesticide charge site isomers using conventional IM and cIM systems.

A growing number of pesticides are being used around the world necessitating strict regulatory policies to guarantee consumer safety. Liquid Chromatography - Mass Spectrometry (LC-MS) is a highly sensitive method for pesticide screening, which provides retention time, mass/charge ratios and the relative abundances of characteristic product ions. Variability in the latter necessitates relatively large tolerances (±30%, SANCO/12682/2019, current EU regulation). One cause of this variability may stem from the presence of different charge-site isomers (charge carrier being a proton, sodium cation, potassium cation and alike); each yielding a set of different product ions, of which the relative ratios are influenced by solution and ion source conditions. Consequently, varying relative abundances may be observed for analyte ions produced from calibration standards, chemical residues in food matrices and across different instruments. Ion Mobility Spectrometry (IMS) is a fast, gas phase separation technique which can resolve charge-site isomers based on differences in their collisional cross sections (CCSs). We previously used the IM device embedded in LC-IM-MS geometry to generate a pesticide CCS database and subsequently focussed upon identification of pesticides which form charge-site isomers. Latterly, we applied this approach to screen food commodities for pesticide residues. In some instances, isomer separation was clear, however sometimes broad, unresolved distributions were observed. Using a high-resolution cyclic IM device (cIM) we resolved and determined CCS values of species of indoxacarb, spinosad, fenpyroximate, epoxiconazole, metaflumizone and avermectin. Furthermore, utilising novel cIM functionalities (tandem-IM) we discovered that two spinosyn sodimers can interconvert in the gas phase.

Cyclic Ion Mobility-Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase.

Ion mobility coupled to mass spectrometry (IM-MS) is widely used to study protein dynamics and structure in the gas phase. Increasing the energy with which the protein ions are introduced to the IM cell can induce them to unfold, providing information on the comparative energetics of unfolding between different proteoforms. Recently, a high-resolution cyclic IM-mass spectrometer (cIM-MS) was introduced, allowing multiple, consecutive tandem IM experiments (IMn) to be carried out. We describe a tandem IM technique for defining detailed protein unfolding pathways and the dynamics of disordered proteins. The method involves multiple rounds of IM separation and collision activation (CA): IM-CA-IM and CA-IM-CA-IM. Here, we explore its application to studies of a model protein, cytochrome C, and dimeric human islet amyloid polypeptide (hIAPP), a cytotoxic and amyloidogenic peptide involved in type II diabetes. In agreement with prior work using single stage IM-MS, several unfolding events are observed for cytochrome C. IMn-MS experiments also show evidence of interconversion between compact and extended structures. IMn-MS data for hIAPP shows interconversion prior to dissociation, suggesting that the certain conformations have low energy barriers between them and transition between compact and extended forms.

LESA Cyclic Ion Mobility Mass Spectrometry of Intact Proteins from Thin Tissue Sections.

Liquid extraction surface analysis (LESA) is an ambient surface sampling technique that allows the analysis of intact proteins directly from tissue samples via mass spectrometry. Integration of ion mobility separation to LESA mass spectrometry workflows has shown significant improvements in the signal-to-noise ratios of the resulting protein mass spectra and hence the number of proteins detected. Here, we report the use of a quadrupole-cyclic ion mobility-time-of-flight mass spectrometer (Q-cIM-ToF) for the analysis of proteins from mouse brain and rat kidney tissues sampled via LESA. Among other features, the instrument allows multiple pass cyclic ion mobility separation, with concomitant increase in resolving power. Single-pass experiments enabled the detection of 30 proteins from mouse brain tissue, rising to 44 when quadrupole isolation was employed. In the absence of ion mobility separation, 21 proteins were detected in rat kidney tissue including the abundant α- and ß-globin chains from hemoglobin. Single-pass cyclic ion mobility mass spectrometry enabled the detection of 60 additional proteins. Multipass experiments of a narrow m/z range (m/z 870-920) resulted in the detection of 24 proteins (one pass), 37 proteins (two passes) and 54 proteins (three passes), thus demonstrating the benefits of improved mobility resolving power.

Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration.

The use of charge-reducing reagents to generate lower-charge ions has gained popularity in the field of native mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS). This is because the lower number of charged sites decreases the propensity for Coulombic repulsions and unfolding/restructuring, helping to preserve the native-like structure. Furthermore, lowering the charge state consequently increases the mass-to-charge values (m/z), effectively increasing spacing between signals originating from small mass differences, such as different proteoforms or protein-drug complexes. IM-MS yields collision cross section (CCS, Ω) values that provide information about the three-dimensional structure of the ion. Traveling wave IM (TWIM) is an established and expanding technique within the native MS field. TWIM measurements require CCS calibration, which is achieved via the use of standard species of known CCS. Current databases for native-like proteins and protein complexes provide CCS values obtained using normal (i.e., non-charge-reducing) conditions. Herein, we explored the validity of using "normal" charge calibrants to calibrate for charge-reduced proteins and show cases where it is not appropriate. Using a custom linear field drift cell that enables the determination of ion mobilities from "first principles", we directly determined CCS values for 19 protein calibrant species under three solution conditions (yielding a broad range of charge states) and two drift gases. This has established a database of CCS and reduced-mobility (K0) values, along with their associated uncertainties, for proteins and protein complexes over a large m/z range. TWIM validation of this database shows improved accuracy over existing methods in calibrating CCS values for charge-reduced proteins.

High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants.

In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.

Carbohydrate isomer resolution via multi-site derivatization cyclic ion mobility-mass spectrometry.

Oligosaccharides serve many roles in extant life and may have had a significant role in prebiotic chemistry on the early Earth. In both these contexts, the structural and isomeric diversity among carbohydrates presents analytical challenges necessitating improved separations. Here, we showcase a chemical derivatization approach, where 3-carboxy-5-nitrophenylboronic acid (3C5NBA) is used to label vicinal hydroxyl groups, amplifying the structural difference between isomers. We explore the applicability of state-of-the-art ion mobility - mass spectrometry (IM-MS) instrumentation in the analysis of derivatized carbohydrates. In particular we focus on the resolving power required for IM separation of derivatized isomers. A recently developed cyclic ion mobility (cIM) mass spectrometer (MS) was chosen for this study as it allows for multi-pass IM separations, with variable resolving power (Rp). Three passes around the cIM (Rp ∼ 120) enabled separation of all possible pairs of four monosaccharide standards, and all but two pairs of eight disaccharide standards. Combining cIM methodology with tandem mass spectrometry (MS/MS) experiments allowed for the major products of each of the 3C5NBA carbohydrate derivatization reactions to be resolved and unequivocally identified.

Isolation of Crude Oil Peaks Differing by m/z ∼0.1 via Tandem Mass Spectrometry Using a Cyclic Ion Mobility-Mass Spectrometer.

Mass spectrometry is widely used in studying the structures of compounds present in crude oil. In this study, a novel mass spectrometer incorporating a cyclic ion mobility separator was used to obtain tandem mass spectra of crude oil compounds in a narrow mass-to-charge ratio (m/z) window. Isolation of specific peaks was performed by combining quadrupole and ion mobility separation. As a result, peaks differing by an m/z value of 0.1 could be isolated. Tandem mass spectrometry with collision-induced dissociation was successfully performed to study the chemical structures of the isolated ions. A series of ions ranging from m/z 374 to m/z 384, differing by two hydrogen atoms but with the same number of carbons, were isolated and tandem mass spectra were obtained. The higher m/z precursor ions produced smaller fragment ions; this is explained by the reduced aromaticity owing to an increased number of hydrogen atoms. The ions at m/z 388 and 374, differing by a CH2 group, produced very similar fragmentation patterns. Overall, the data obtained from this study clearly demonstrate that the novel cyclic ion mobility-mass spectrometer is a powerful instrument that can provide tandem mass spectra of individual compounds constituting complex mixtures such as crude oils.

Structure Determination of Large Isomeric Oligosaccharides of Natural Origin through Multipass and Multistage Cyclic Traveling-Wave Ion Mobility Mass Spectrometry.

Carbohydrate isomers with identical atomic composition cannot be distinguished by mass spectrometry. By separating the ions according to their conformation in the gas phase, ion mobility (IM) coupled to mass spectrometry is an attractive approach to overcome this issue and extend the limits of mass spectrometry in structural glycosciences. Recent technological developments have significantly increased the resolving power of ion mobility separators. One such instrument features a cyclic traveling-wave IM separator integrated in a quadrupole/time-of-flight mass spectrometer. This system allows for multipass ion separations and for pre-, intra-, and post-IM fragmentation. In the present study, we utilize this system to explore a complex mixture of oligoporphyrans derived from the enzymatic digestion of the cell wall of the red alga P. umbilicalis. We are able to deduce their complete structure using IM arrival times and the m/z of specific fragments. This approach was successfully applied for sequencing of oligoporphyrans of up to 1500 Da and included the positioning of the methyl ether and sulfate groups. The structures defined in this study by IM-MS/MS agree with those found in the past but use much more time-consuming analytical approaches. This study also revealed some so far undescribed structures, present at very low abundance. In addition, the results made it possible to compare the abundance of the different isomers released by the enzyme and to draw further conclusions on the specificity of ß-porphyranase and more particularly on its accommodation tolerance of anhydro-bridges in subsites. Finally, a separation of two isomers with very similar mobility was obtained after 58 passes around the cIM, with an estimated resolving power of 920 for these triply charged species, confirming the structures attributed to these two isomers.

Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device.

Ion mobility mass spectrometry (IM-MS) allows separation of native protein ions into "conformational families". Increasing the IM resolving power should allow finer structural information to be obtained and can be achieved by increasing the length of the IM separator. This, however, increases the time that protein ions spend in the gas phase and previous experiments have shown that the initial conformations of small proteins can be lost within tens of milliseconds. Here, we report on investigations of protein ion stability using a multipass traveling wave (TW) cyclic IM (cIM) device. Using this device, minimal structural changes were observed for Cytochrome C after hundreds of milliseconds, while no changes were observed for a larger multimeric complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF) also enables complex tandem IM experiments to be performed, which were used to obtain more detailed collision-induced unfolding pathways for Cytochrome C. The instrument geometry provides unique capabilities with the potential to expand the field of protein analysis via IM-MS.

A Cyclic Ion Mobility-Mass Spectrometry System.

Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS n, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.

Cyclic Ion Mobility Mass Spectrometry Distinguishes Anomers and Open-Ring Forms of Pentasaccharides.

There is increasing biopharmaceutical interest in oligosaccharides and glycosylation. A key requirement for these sample types is the ability to characterize the chain length, branching, type of monomers, and importantly stereochemistry and anomeric configuration. Herein, we showcase the multi-function capability of a cyclic ion mobility (cIM) separator embedded in a quadrupole/time-of-flight mass spectrometer (Q-ToF MS). The instrument design enables selective activation of mobility-separated precursors followed by cIM separation of product ions, an approach analogous to MSn. Using high cIM resolution, we demonstrate the separation of three isomeric pentasaccharides and, moreover, that three components are present for each compound. We show that structural differences between product ions reflect the precursor differences in some cases but not others. These findings are corroborated by a heavy oxygen labelling approach. Using this methodology, the identity of fragment ions may be assigned. This enables us to postulate that the two main components observed for each pentasaccharide are anomeric forms. The remaining low abundance component is assigned as an open-ring form.

Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy.

The early stages of fibril formation are difficult to capture in solution. We use cold-ion spectroscopy to examine an 11-residue peptide derived from the protein transthyretin and clusters of this fibre-forming peptide containing up to five units in the gas phase. For each oligomer, the UV spectra exhibit distinct changes in the electronic environment of aromatic residues in this peptide compared to that of the monomer and in the bulk solution. The UV spectra of the tetra- and pentamer are superimposable but differ significantly from the spectra of the monomer and trimer. Such a spectral evolution suggests that a common structural motif is formed as early as the tetramer. The presence of this stable motif is further supported by the low conformational heterogeneity of the tetra- and pentamer, revealed from their IR spectra. From comparison of the IR-spectra in the gas and condensed phases, we propose putative assignments for the dominant motif in the oligomers.

Structurally Flexible and Solution Stable [Ln4TM8(OH)8(L)8(O2CR)8(MeOH)y](ClO4)4: A Playground for Magnetic Refrigeration.

The family of compounds of general formula [LnIII4TMII8(OH)8(L)8(O2CR)8(MeOH)y](ClO4)4 {[Gd4Zn8(OH)8(hmp)8(O2CiPr)8](ClO4)4 (1a); [Y4Zn8(OH)8(hmp)8(O2CiPr)8](ClO4)4 (1b); [Gd4Cu8(OH)8(hmp)8(O2CiPr)8](ClO4)4 (2a); [Y4Cu8(OH)8(hmp)8(O2CiPr)8](ClO4)4 (2b); [Gd4Cu8(OH)8(hep)8(O2CiPr)8](ClO4)4 (3a); [Gd4Cu8(OH)8(Hpdm)8(O2CtBu)8](ClO4)4 (4a); [Gd4Cu8(OH)8(ea)8(O2CMe)8](ClO4)4 (5a); [Gd4Ni8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (6a); [Y4Ni8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (6b); [Gd4Co8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (7a); [Y4Co8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (7b)} can be formed very simply and in high yields from the reaction of Ln(NO3)3·6H2O and TM(ClO4)2·6H2O and the appropriate ligand blend in a mixture of CH2Cl2 and MeOH in the presence of a suitable base. Remarkably, almost all the constituent parts, namely the lanthanide (or rare earth) ions LnIII (here Ln = Gd or Y), the transition metal ions TMII (here TM = Zn, Cu, Ni, Co), the bridging ligand L (Hhmp = 2-(hydroxymethyl)pyridine; Hhep = 2-(hydroxyethyl)pyridine; H2pdm = pyridine-2,6-dimethanol; Hea = 2-ethanolamine), and the carboxylates can be exchanged while maintaining the structural integrity of the molecule. NMR spectroscopy of diamagnetic complex 1b reveals the complex to be fully intact in solution with all signals from the hydroxide, ligand L, and the carboxylates equivalent on the NMR time scale, suggesting the complex possesses greater symmetry in solution than in the solid state. High resolution nano-ESI mass spectrometry on dichloromethane solutions of 2a and 2b shows both complexes are present in two charge states with little fragmentation; with the most intense peak in each spectrum corresponding to [Ln4Cu8(OH)8(hmp)8(O2CiPr)8](ClO4)22+. This family of compounds offers an excellent playground for probing how the magnetocaloric effect evolves by introducing either antiferromagnetic or ferromagnetic interactions, or magnetic anisotropy, by substituting the nonmagnetic ZnII (1a) with CuII (2a), NiII (6a) or CoII (7a), respectively. The largest magnetocaloric effect is found for the ferromagnetically coupled complex 6a, while the predominant antiferromagnetic interactions in 2a yield an inverse magnetocaloric effect; that is, the temperature increases on lowering the applied field, under the proper experimental conditions. In spite of increasing the magnetic density by adding ions that bring in antiferromagnetic interactions (2a) or magnetic anisotropy (7a), the magnetocaloric effect is overall smaller in 2a and 7a than in 1a, where only four GdIII spins per molecule contribute to the magnetocaloric properties.

New High Resolution Ion Mobility Mass Spectrometer Capable of Measurements of Collision Cross Sections from 150 to 520 K.

We present a new variable temperature (VT), high resolution ion mobility (IM) drift tube coupled to a commercial mass spectrometer (MS). Ions are generated in an electrospray ion source with a sampling cone interface and two stacked ring RF guides which transfer ions into the mobility analyzer located prior to a quadrupole time-of-flight mass spectrometer. The drift cell can be operated over a pressure range of 0.5-3 Torr and a temperature range of 150-520 K with applied fields typically between 3 and 14 V cm-1. This makes the instrument suitable for rotationally averaged collision cross section (CCS) measurements at low E/N ratios where ions are near thermal equilibrium with the buffer gas. Fundamental studies of the effective ion temperatures can be performed at high E/N ratios. An RF ion trap/buncher is located at the beginning of the drift region, which modulates the continuous ion beam into spatially narrow packets. Packets of ions then drift in a linear electric field, which is 50.5 cm long, and are separated according to their mobility in an inert buffer gas. Post-drift, an ion funnel focuses the radially spread pulses of ions into the inlet of a commercial MS platform (Micromass QToF2). We present the novel features of this instrument and results from VT-IM-MS experiments on a range of model systems-IMS CCS standards (Agilent ESI Tune Mix), the monomeric protein Ubiquitin (8.6 kDa), and the tetrameric protein complex Concanavalin A (103 kDa). We evaluate the performance of the instrument by comparing ambient DTCCSHe values of model compounds with those found in the literature. Several effects of temperature on collision cross sections and resolution are observed. For small rigid molecules, changes in resolution are consistent with anticipated thermal diffusion effects. Changes in measured DTCCSHe for these rigid systems at different temperatures are attributed primarily to the effect of temperature on the long-range attractive interaction. Similar effects are seen for protein ions at low temperatures, although there is also some evidence for structural transitions. By heating the protein ions, their conformational profiles are significantly altered. Very high temperatures narrow the conformational space presented by both Ubiquitin and Concanavalin; it appears that diverse conformational families are "melted" into more homogeneous populations. Because of this conformational heterogeneity, the apparent IMS resolution obtained for proteins at ambient and reduced temperatures is an order of magnitude lower than the expected diffusion limited resolution (Rmax). This supports a hypothesis that the broad DTCCSHe features frequently observed for proteins do not correspond to interconverting conformers, but rather to high numbers of intrinsically stable structures.

Sizing and Discovery of Nanosized Polyoxometalate Clusters by Mass Spectrometry.

Ion mobility-mass spectrometry (IM-MS) is a powerful technique for structural characterization, e.g., sizing and conformation, particularly when combined with quantitative modeling and comparison to theoretical values. Traveling wave IM-MS (TW-IM-MS) has recently become commercially available to nonspecialist groups and has been exploited in the structural study of large biomolecules, however reliable calibrants for large anions have not been available. Polyoxometalate (POM) species-nanoscale inorganic anions-share many of the facets of large biomolecules, however, the full potential of IM-MS in their study has yet to be realized due to a lack of suitable calibration data or validated theoretical models. Herein we address these limitations by reporting DT-IM (drift tube) data for a set of POM clusters {M12} Keggin 1, {M18} Dawson 2, and two {M7} Anderson derivatives 3 and 4 which demonstrate their use as a TW-IM-MS calibrant set to facilitate characterization of very large (ca. 1-4 nm) anionic species. The data was also used to assess the validity of standard techniques to model the collision cross sections of large inorganic anions using the nanoscale family of compounds based upon the {Se2W29} unit including the trimer, {Se8W86O299} A, tetramer, {Se8W116O408} B, and hexamer {Se12W174O612} C, including their relative sizing in solution. Furthermore, using this data set, we demonstrated how IM-MS can be used to conveniently characterize and identify the synthesis of two new, i.e., previously unreported POM species, {P8W116}, unknown D, and {Te8W116}, unknown E, which are not amenable to analysis by other means with the approximate formulation of [H34W118X8M2O416](44-), where X = P and M = Co for D and X = Te and M = Mn for E. This work establishes a new type of inorganic calibrant for IM-MS allowing sizing, structural analysis, and discovery of molecular nanostructures directly from solution.

Making hybrid [n]-rotaxanes as supramolecular arrays of molecular electron spin qubits.

Quantum information processing (QIP) would require that the individual units involved--qubits--communicate to other qubits while retaining their identity. In many ways this resembles the way supramolecular chemistry brings together individual molecules into interlocked structures, where the assembly has one identity but where the individual components are still recognizable. Here a fully modular supramolecular strategy has been to link hybrid organic-inorganic [2]- and [3]-rotaxanes into still larger [4]-, [5]- and [7]-rotaxanes. The ring components are heterometallic octanuclear [Cr7NiF8(O2C(t)Bu)16](-) coordination cages and the thread components template the formation of the ring about the organic axle, and are further functionalized to act as a ligand, which leads to large supramolecular arrays of these heterometallic rings. As the rings have been proposed as qubits for QIP, the strategy provides a possible route towards scalable molecular electron spin devices for QIP. Double electron-electron resonance experiments demonstrate inter-qubit interactions suitable for mediating two-qubit quantum logic gates.