Ion Mobility Mass Spectrometry

We are very pleased to present this issue of Analyst, devoted to the exciting and dynamic science currently underway in the area of ‘ion mobility-mass spectrometry’ (IM-MS). We have each devoted over 15 years of our respective careers to this field of inquiry, and have been awestruck by the advancements in both technique and technology that have taken place in that time. This has been matched by an explosion in the use and application of ion mobility mass spectrometry, when we started it was the domain of a few groups prepared to build their own instruments, whereas it is now a ‘goto’ technique for analysis with several commercially available options. The 27 papers included in this themed issue, including 2 Minireviews and 1 Communication, span an impressive catalog of scientific topics, ranging from computational chemistry to structural biology. In addition, the investigators highlighted in this themed issue represent both well-established IM-MS laboratories, as well as new players in this dynamic area. The breadth and depth of the science reported in this themed issue surely predicts a bright and healthy future for IM-MS in the years to come!

The Minireviews contained within this themed issue cover two important IM-MS application areas: enabling next-generation medical diagnostics and the characterization of structural heterogeneity – both in solution and in the gas phase. A variety of approaches, ranging from gas chromatography to eNoses, have been employed in the evaluation of gas-phase biomarkers that emanate from many types of clinical samples. In their Minireview, Covington and colleagues (c5an00868a) evaluate the potential impact of field-asymmetric ion mobility spectrometry (FAIMS) as a new approach toward such biomarker analyses, and find considerable evidence suggesting that such technologies have the ability to fill gaps in measurement capacity left by existing approaches. Similarly, complex synthetic and biological polymers exhibit rough conformational landscapes in the gas phase that have provided challenging yet fertile ground for the growth of new IM-MS methods. Valentine and co-workers (c5an00922g) review the last 10 years of the IM-MS literature to highlight the power and promise of this technology for peeling back the layers of structural complexity found in both key targets of synthetic design and molecular biochemistry.

New computational approaches for interpreting IM-MS data feature prominently in papers from Bleiholder (c5an00712g) and Lapthorne et al. (c5an00411j). In the former work, some of the key challenges in computing estimates of ion-neutral collision cross sections (CCSs) in nitrogen drift gas are undertaken. The author introduces and evaluates a local collision probability approximation (LCPA) which improves on both the efficiency and flexibility of previous algorithms for the estimation of analyte ion CCS. In the latter work, the authors broadly evaluate the agreement between density functional theory (DFT)-derived models for drug-like small molecules and their experimentally-determined CCS values, with the goal of bench-marking existing computational/experimental strategies. The authors find excellent agreement between experimentally-determined CCS values and model structures when an empirically-derived correction factor is employed that accounts for ion-neutral interaction parameterization deficits that exist within current algorithms aimed at computing CCSs of small-molecule model structures.

The section on IM-MS instrumentation and theory contains three wonderful submissions all of which demonstrate significant ongoing efforts in this area. The group of McLean, May and co-workers (c5an00923e) has a beautiful paper which contrasts conditional with semi-empirical resolving power theories and compares both with experiments performed in three different drift gases. The submission from Kurulugama et al. (c5an00991j) also examines the performance of a high resolution ion mobility instrument, using different drift gases and compares the collision cross sections achieved for 275 total pesticides including structural isomers in five different drift gases. Smith and his team also consider the resolving power of ion mobility, but in this case based on a very novel form of ion separation devices termed ‘Structures for Lossless Ion Manipulations’ or SLIM! (c5an00844a). Such devices are fabricated using printed-circuit board (PCB) technologies and this work presents refinements in the design that reduce the loss of ions whilst maintaining resolution.

In conjunction with the instrumentation described above, many of the papers contained in this issue describe new methods of gathering IM-MS data that improve the resolving power, accuracy, or signal-to-noise ratio (SNR) of the resulting datasets. For example, in a paper from Fernandez et al. (c5an00946d) a new CCS calibration strategy for the traveling wave ion mobility spectrometry (TWIMS) analysis of negative ions is demonstrated to produce highly accurate and precise values, likely enabling broader TWIMS applications toward negatively-charged analytes. In a paper from Clowers and colleagues (c5an00941c), a new Fourier Transform (FT)-IM-MS approach is described, capable of improving the SNR of IM-MS data by an order of magnitude through the innovative use of a 180° out-of-phase pulse sequence and a single ion gate that improves upon previous FT-IM-MS designs. In addition, Glish et al. (c5an00845j) describe a new linked scan methodology for FAIMS operation that enhances the effective resolving power to over 7900, a value over 16 times greater than those reported previously for this technology.

The developments in resolving power and separation described above are key when applied to the analysis of small molecules and in particular for isomer and complex mixture separation. This latter capability of IMS is crucial in the work of Cooper et al. (c5an00933b) who demonstrate the benefit of employing high field asymmetric waveform ion mobility spectrometry (FAIMS) for the analysis of molecules from dried blood spots on filter paper following Liquid Extraction Surface Analysis (LESA). Solouki and co-workers introduce a chemometric method to deconvolute collision-induced dissociation data which are obtained post-IM separation (c5an00940e). They demonstrate the use of this with trisacharides and peptides. Campbell, Hopkins and colleagues apply differential mobility spectrometry (DMS) to separate quinoline-based drugs (c5an00842e). In this fine study they present a systematic evaluation of ion microsolvation by considering the behavior of differently substituted quinolinium ions as they cluster and decluster with different solvents and counter ions in the DMS cell. Groessl, Knochenmuss and Graf also demonstrate the benefits of IMS in the analysis of complex mixtures (c5an00838g). They apply high resolution IMS both to separate and identify isomeric lipids: differing only in the position of the acyl chain they examine both standard preparations as well as biological fluids and in the latter see no loss of performance. As with the Cooper study, this work highlights the potential of IMS in clinical analysis.

Similarly to the experiments described above focusing on isomer separation, this issue contains a number of reports aimed at detailed structural characterizations and separations of carbohydrate ions. In a contribution from Dodds and Huang (c5an01093d), the structures of multiple carbohydrate isomers adducted to group II metal ions are probed using IM-MS and electron transfer dissociation (ETD), revealing CCS differences between many such adducted isomers that are not present in their typically-produced protonated forms. In a another paper targeting carbohydrate isomer differentiation, Clemmer and colleagues (c5an00840a) report on a tandem IM method coupled with collision-induced dissociation (CID), and present data for a wide-ranging group of analytes demonstrating a broad ability to distinguish isomeric sugars. In a final carbohydrate-themed communication, Pagel, Struwe and colleagues (c5an01092f) present a negative ion dataset for a series of high-mannose content glycans, revealing a surprising level of conformational polydispersity not observed in positively-charged analogs.

Peptides have long been a subject of study for ion mobility mass spectrometry, and the next section of papers continues in this tradition with some remarkable new insights. Russell et al. examine the effect of charge state and protonatable side chain location on the gas-phase conformation of model peptides using both ion mobility and extensive molecular modeling (c5an00826c). They rationalize the occurrence of helices based on the location of the basic side chain, and find for AK_n ions, there is a strong preference for helical conformations near the N-terminus and for charge-solvated conformations near the C-terminus. Hogan et al. model the effect of vapor uptake induced mobility shifts in peptides that have been seen to occur with the recently developed transversal modulation ion mobility spectrometry (TMIMS) technique (c5an00753d). They show that the shifts in peptide ions rapidly move to lower values at low saturation ratios, and that the shifts then cease with increasing saturation ratio, and caution that further model development will be needed to best explain the data from studies of this type. The final paper in this section from Baker and co-workers show the benefit of using ultraFAIMS coupled with low field ion mobility mass spectrometry to provide three-dimensions of separation for complex, bottom-up proteomic analyses (c5an00897b). The immense power of this platform for targeted protein analysis at the peptide level, which enables separation of isometric species and of peptides that would be otherwise obscured in 1-D or 2-D separations, is exemplified in this exquisite study.

Climbing steadily up the molecular weight ladder, the structures and folding processes linked to intact proteins is a focal point for many of the contributing authors featured here. For example, Park and colleagues (c5an00841g) utilize high resolution trapped ion mobility spectrometry (TIMS) to investigate the gas-phase structures of ubiquitin ions, as well as illustrate the structural heterogeneity of such small, thermally-labile proteins in the gas phase. In a set of experiments aimed at recording transient protein folding events in solution, Wilson et al. (c5an00843c) describe time-resolved IM-MS data which reveal evidence that cytochrome c populates equivalent intermediate forms when folding is observed either using equilibrium conditions or under kinetic control. Shifting focus to non-covalent protein complexes, work contributed by Amster et al. (c5an00908a) validates the use of IM-MS to accurately record the structural changes of Antithrombin III upon binding a range of therapeutically-relevant glycosaminoglycan ligands.

The final set of papers contains work on complex protein assemblies. The groups of both Ashcroft and Barran have contributed articles which use ion mobility mass spectrometry to examine oligomeric aggregating proteins. Ashcroft, Radford et al. focus on the copolymerization of IAPP (amylin) and the Aβ peptide and show that co-assembly of the two sequences results in hetero-oligomers with distinct structural features possessing aggregation kinetics properties that differ from those shown by the homo-oligomers present in solution (c5an00865d). The contribution from the team of Barran and MacPhee focuses on the first stages of the assembly of amyloid fibrils using the model system insulin (c5an01253h). They show insulin oligomers [I]_n where n ranges from 1 to 12, and ion mobility analysis reveals around 60 structurally distinct species across this oligomer distribution. Experimental data are then used to train molecular dynamics (MD) simulations to characterize a persistent prefibrillar protein oligomer (here a β-sheet-enriched dimer). Both studies will be used to inform models of nucleation and growth, as well as providing an attractive method to test therapeutic agents against these structural intermediates. Wysocki et al. have contributed an insightful article on the use of surface-induced dissociation (SID) coupled with ion mobility mass spectrometry to provide insights into protein assembly and the topology of homomeric and heteromeric protein complexes (c5an01095k). In particular they show the detailed understanding of the distribution of charge states upon complex disassembly that can be gained with two stages of SID, one before and one after mobility separation. The final manuscript in our themed issue comes again from one of us! Ruotolo and Bornschein have also examined multiprotein complexes and here they cleverly and systematically manipulate charge states and experimental conditions with ion–ion chemistry to allow collision-induced ejection of compact, rather than unfolded, protein subunits (c5an01242b). This work, along with many others in this collection, epitomizes the ability of ion mobility mass spectrometry to provide unique insights into structural biology by distinguishing both stoichiometry and conformational heterogeneity as well as complex stability within a single experiment.

In summing up our introduction to this themed issue we would like to offer our profound thanks to all the contributors: we know that many of you will have worked hard, long hours to obtain the beautiful data, to develop new theoretical insights and to build the novel instruments, all of which have provided the outstanding results collected in this issue. It doesn't end here: we have several more contributions that did not quite make the deadline for the paper issue but will be assembled along with these papers in the collection available on-line. We would also like to thank Matt Cude for pushing this idea in the start and all of the editorial team at Analyst who have worked tirelessly to get the papers reviewed and published in a timely and fair manner. We have been thoroughly honored to edit this issue, and it remains to encourage the readers to read it and be inspired for fruitful future studies involving this enabling technique.

Perdita Barran

University of Manchester, UK

Brandon Ruotolo

University of Michigan, Ann Arbor, MI, USA

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