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Cyclable Variable Path Length Multilevel Structures for Lossless Ion Manipulations (SLIM) Platform for Enhanced Ion Mobility Separations
Ion mobility-mass spectrometry (IMS-MS) is increasingly used to analyze complex samples and provide structural information of unknown compounds. As the complexity of samples increases, there is a need to improve the resolution of IMS-MS instruments to increase the rate of molecular identification. In this work, we evaluated a cyclable and variable-pathlength multilevel Structures for Lossless Ion Manipulations (SLIM) platform to achieve a higher resolving power than previously possible. This new multilevel SLIM platform has eight separation levels connected by ion escalators and a path length of ~88 meters (~11 meters per level). Our new multilevel SLIM can also be operated in an ‘ion cycling’ mode where a set of return ion escalators transport ions from the eighth back to the first level, allowing even longer path lengths (and higher IMS resolution). The platform has been improved to enhance the ion transmission and IMS separation quality by reducing the spacing between SLIM boards as well as board thickness, reducing the ions’ escalator residence time. Compared to the previous generation, the new multilevel SLIM demonstrated a better transmission for a set of phosphazene ions, especially for the low-mobility ions. The new multilevel SLIM achieved better resolving powers than our previous 4-level SLIM. The collision cross-section-based resolving power of the SLIM platform was tested using a pair of singly-charged reverse sequence peptides (SDGRG 1+ , GRGDS 1+ ). We achieved 1100 resolving power using 88 meters of path length (i.e., 8 levels) and 1400 following an additional pass through the eight levels (i.e., 16 levels or 173.5 m). The multilevel SLIM was further evaluated to demonstrate the enhanced separation for a positively and negatively charged brain total lipid extract sample. Finally, the new multilevel SLIM enables much higher resolving powers for a wide range of ion mobilities, improved transmission for low-mobility ions, and the ability to perform even higher resolving power for ions of interest.
Fundamental studies of gas phase ionic reactions by ion mobility spectrometry
Ion mobility spectrometry (IMS) provides a promising approach to the study of gas phase ionic reactions in buffer gases at unusually high pressures. This point is illustrated here by studies of the Sn2 nucleophilic displacement reaction, Cl(-) + CH3Br yields Br + CH3Br, using IMS at atmospheric pressure. The equilibrium clustering reaction, Cl(-)(CHCI3)(n - 1) + CHCI3 yields Cl(-)(CHCI3)(n), where n = 1 and 2, and the effect of clustering on the Sn2 reaction with CH3Br have also been characterized by this IMS-based kinetic method. Present problems and anticipated improvements in the application of ion mobility spectrometry to studies of other gas phase ionic processes are discussed.
Ion Mobility Spectrometry with High Ion Utilization Efficiency Using Traveling Wave-Based Structures for Lossless Ion Manipulations
Ion packets introduced from gates, ion funnel traps, and other conventional ion injection mechanisms produce ion pulse widths typically around a few microseconds or less for ion mobility spectrometry (IMS)-based separations on the order of 100 milliseconds. When such ion injection techniques are coupled with ultralong path length traveling wave (TW)-based IMS separations (i.e., on the order of seconds) using structures for lossless ion manipulations (SLIMs), typically very low ion utilization efficiency is achieved for continuous ion sources [e.g., electrospray ionization (ESI)]. Even with the ability to trap and accumulate much larger populations of ions than being conventionally feasible over longer time periods in SLIM devices, the subsequent long separations lead to overall low ion utilization. In this study, we report the use of a highly flexible SLIM arrangement, enabling concurrent ion accumulation and separation and achieving near-complete ion utilization with ESI. We characterize the ion accumulation process in SLIM, demonstrate >98% ion utilization, and show both increased signal intensities and measurement throughput. This approach is envisioned to have broad utility to applications, for example, involving the fast detection of trace chemical species.
High-resolution ion mobility based on traveling wave structures for lossless ion manipulation resolves hidden lipid features
Abstract High-resolution ion mobility (resolving power > 200) coupled with mass spectrometry (MS) is a powerful analytical tool for resolving isobars and isomers in complex samples. High-resolution ion mobility is capable of discerning additional structurally distinct features, which are not observed with conventional resolving power ion mobility (IM, resolving power ~ 50) techniques such as traveling wave IM and drift tube ion mobility (DTIM). DTIM in particular is considered to be the “gold standard” IM technique since collision cross section (CCS) values are directly obtained through a first-principles relationship, whereas traveling wave IM techniques require an additional calibration strategy to determine accurate CCS values. In this study, we aim to evaluate the separation capabilities of a traveling wave ion mobility structures for lossless ion manipulation platform integrated with mass spectrometry analysis (SLIM IM-MS) for both lipid isomer standards and complex lipid samples. A cross-platform investigation of seven subclass-specific lipid extracts examined by both DTIM-MS and SLIM IM-MS showed additional features were observed for all lipid extracts when examined under high resolving power IM conditions, with the number of CCS-aligned features that resolve into additional peaks from DTIM-MS to SLIM IM-MS analysis varying between 5 and 50%, depending on the specific lipid sub-class investigated. Lipid CCS values are obtained from SLIM IM ( TW(SLIM) CCS) through a two-step calibration procedure to align these measurements to within 2% average bias to reference values obtained via DTIM ( DT CCS). A total of 225 lipid features from seven lipid extracts are subsequently identified in the high resolving power IM analysis by a combination of accurate mass-to-charge, CCS, retention time, and linear mobility-mass correlations to curate a high-resolution IM lipid structural atlas. These results emphasize the high isomeric complexity present in lipidomic samples and underscore the need for multiple analytical stages of separation operated at high resolution. Graphical abstract
Ion Mobility Separations Using Cocentric Architecture
Ion mobility separations are usually performed in linear channels, which, when extended, can have a large footprint. In this work, we explored the performance of an ion mobility device with a curved architecture which can have a more compact form. The Co-centric Ion Mobility Spectrometer (CIMS) works by manipulating ions between two co-centric surfaces, each containing a serpentine track. The mobility separation inside CIMS is achieved using traveling waveforms (TWs). We initially evaluated the device using ion trajectory simulations using SIMION, which indicated that when ions traveled circularly inside CIMS, they resulted in similar resolving powers and transmitted m/z range as traveling in a straight path in structures for lossless ion manipulations (SLIM). We then performed experimental validation of CIMS in conjunction with a TOF MS. The CIMS was made of 2 flexible printed circuit board materials folded into concentric cylinders separated by a gap of 2.8 mm. The device was about 50 mm diameter × 152 mm long and provided 1.846 m of serpentine path length. Three sets of mixtures (Agilent tune mixture, tetraalkylammonium salts, and 8 peptide mixture) and four traveling waveform profiles (square, sine, triangle, and sawtooth) were used. The sawtooth TW profile produced a slightly higher resolving power for the Agilent tuning mixture and tetraalkylammonium ions. The average resolving power for Agilent tune mixture ions ranged from 37 (using sawtooth TW) to 27 (using square TW). For tetraalkylammonium ions, the average resolving powers ranged from 45 (sawtooth TW) to 31 (square TW). For the peptide mixture ions, the resolving power was similar among the four TW profiles and ranged from 51 to 56. The average percent error in TW CCS for the peptide mixture ions ranged was about 0.4%. In conclusion, the new device showed promising results for a device made of a flexible printed circuit board material, but improvements are needed to further increase the resolving power.
Dynamic time-warping correction for shifts in ultrahigh resolving power ion mobility spectrometry and structures for lossless ion manipulations
Detection of arrival time shifts between ion mobility spectrometry (IMS) separations can limit achievable resolving power (Rp), particularly when multiple separations are summed or averaged, as commonly practiced. Such variations are more apparent in higher Rp measurements, and are particularly evident in long path length traveling wave structures for lossless ion manipulations (SLIM) IMS due to their typically much longer separation times. Here we explore the utility of a data processing approaches employing linear alignment (LA) and nonlinear dynamic time warping (DTW) of IMS separations to correct for variations between separations, such as due to pressure fluctuations. For multipass SLIM IMS separations, where narrow mobility range measurements have arrival times that can extend to several seconds, the LA approach effectively corrected for such variations, and significantly improvement Rp for summed separations. However, LA was much less effective for high Rp broad mobility range separations, such as obtained with multilevel SLIM IMS. Changes in IMS arrival times ions were observed to be correlated with small pressure changes, with approximately 0.6% relative arrival time shifts being common, sufficient to result in a loss of Rp for summed separations. Comparison of the approaches showed DTW alignment performed similarly to LA when used over a narrow mobility range, but was significantly better (providing narrower peaks and higher signal intensities) for wide mobility range data. We found the DTW approach increased Rp by as much as 115% for measurements in which 50 IMS separations over 2 seconds were summed, and leading to a large improvement in effective Rp. We conclude that DTW is superior to LA for ultrahigh resolution broad mobility range SLIM IMS separations, correcting for ion arrival time shifts regardless of the cause. Our tool is publicly available for use with universal ion mobility format (.UIMF) and text (.txt) files.
Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations
The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling waves ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively-charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20 V0-p, 25 V0-p, and 30 V 0-p ). The calibration errors for the three calibrant sets Agilent tuning mixture and polyalanine, and one assembled in-house showed negligible differences using a sine-shaped TW waveform. Furthermore, calibration errors were all within 1-2 % of the DTIMS measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh resolution multi-pass (long path length) SLIM TWIMS demonstrated improved CCS calibration for phospholipid and bile acid isomers.
Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry–Mass Spectrometry
Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. In conclusion, we first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.
Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations
Structures for lossless ion manipulations (SLIM) have recently enabled a powerful implementation of traveling wave ion mobility spectrometry (TWIMS) for ultra-high resolution separations. However, optimization of experimental parameters remains challenging. Most TWIMS separations have utilized square-shaped waveforms applied by time-dependent voltage stepping across a repeating sets of electrodes; however, alternative waveforms may provide further improvements to resolution. In this work, we characterize five waveforms (including square and sine) in terms of their transmission efficiency, IMS resolution, and resolving power, and explore the effects of TW amplitude and speed on the performance of each. We found, consistent with previous work, separations were generally improved with higher TW amplitudes, moderately improved by lower speeds (limited by ion ‘surfing’ with the waves), and found decreases in signal intensity at the extremes of operating conditions. The triangle and asymmetric ‘ramp forward’ shaped profiles were found to provide modestly greater resolution and resolving power, an observation we tentatively attribute to their relatively uniform fields and minimal low-field regions.
A Miniature Multilevel Structures for Lossless Ion Manipulations Ion Mobility Spectrometer with Wide Mobility Range Separation Capabilities
Here, ion mobility spectrometry employing structures for lossless ion manipulations (SLIM-IMS) is an attractive gas-phase separation technique due to its ability to achieve unprecedented effective ion path lengths (>1 km) and IMS resolving powers in a small footprint. The emergence of multilevel SLIM technology, where ions are transferred between vertically stacked SLIM electrode surfaces, has subsequently allowed for ultralong single pass path lengths (>40 m) to be achieved, enabling ultrahigh resolution IMS measurements to be performed over the entire mobility range in a single experiment. The implementation of multiple SLIM levels requires very little additional space for the SLIM system, and we developed a miniature SLIM module (miniSLIM) based on multilevel SLIM technology and report the performance here. The module is 11.1 cm x 6.7 cm x 1.4 cm (L x W x H) and consists of three SLIM levels totaling 1-meter path length. Ion trajectory simulations were used to optimize the SLIM board spacings and SLIM board thicknesses of the miniSLIM IMS system. Methods of efficiently transferring ions between SLIM levels were examined and a new approach using asymmetric traveling waves (TWs) was developed and implemented in the miniSLIM. We experimentally characterized the performance of the --meter multilevel miniSLIM IMS-MS relative to a drift tube IM--MS using an Agilent tuning mixture and tetraalkylammonium cations. The 1-meter miniSLIM achieved a resolving power of up to 131 (CCS/ΔCCS), ~1.5x higher than achievable with a 78 cm path length drift tube IMS, and successfully transmitted the entire ion mobility range in a single separation. We also demonstrated the miniSLIM’s performance as a standalone IMS system (i.e., without MS), showing baseline separation between Agilent tuning mixture cations with the full mobility range observed, and a standard peptide mixture with different charge states readily differentiated. Overall the miniSLIM provides a compact alternative to high performance IMS instruments possessing similar path lengths.
Third International Workshop on Ion Mobility Spectrometry
Basic research in ion mobility spectrometry has given rise to rapid advancement in hardware development and applications. The Third International Workshop on Ion Mobility Spectrometry (IMS) was held October 16-19, 1994, at Johnson Space Center to provide a forum for investigators to present the most recent results of both basic and applied IMS research. Presenters included manufacturers and various users, including military research organizations and drug enforcement agencies. Thirty papers were given in the following five sessions: Fundamental IMS Studies, Instrument Development, Hyphenated IMS Techniques, Applications, and Data Reduction and Signal Processing. Advances in hardware development, software development, and user applications are described.
Analysis of Ultra-Pure Gases by Ion Mobility Spectrometry
Work has continued with the evaluation of the Ion Mobility Spectrometer (IMS) for the analysis of gases having low parts-per-billion (10(exp -9)) water concentration. A modified PCP, inc. MMS-160 Mobility Mass Spectrometer System was used for the analysis of ultra-pure argon and nitrogen. The MMS-160 system permits the mass-identification of unique reactant and product ions observed in the reduced-water host gases. When the water is removed to low ppb levels, higher energy reactant ions are observed. In nitrogen, distinct odd- and even-numbered nitrogen cluster ion mobility peaks are observed, as well as adduct ion peaks from the trace contaminants in the gas. Argon also produces a cluster ion mobility peak and adduct ion peaks from trace components in the gas. Levels of contaminants in these ultra-pure gases can be determined from the ion mobility spectra. A calibrated source was used to provide variable known quantities of water to the pure gas supply of the IMS.
Miniature Ion-Mobility Spectrometer
The figure depicts a proposed miniature ion-mobility spectrometer that would be fabricated by micromachining. Unlike prior ion-mobility spectrometers, the proposed instrument would not be based on a time-of-flight principle and, consequently, would not have some of the disadvantageous characteristics of prior time-of-flight ion-mobility spectrometers. For example, one of these characteristics is the need for a bulky carrier-gas-feeding subsystem that includes a shutter gate to provide short pulses of gas in order to generate short pulses of ions. For another example, there is need for a complex device to generate pulses of ions from the pulses of gas and the device is capable of ionizing only a fraction of the incoming gas molecules; these characteristics preclude miniaturization. In contrast, the proposed instrument would not require a carrier-gas-feeding subsystem and would include a simple, highly compact device that would ionize all the molecules passing through it. The ionization device in the proposed instrument would be a 0.1-micron-thick dielectric membrane with metal electrodes on both sides. Small conical holes would be micromachined through the membrane and electrodes. An electric potential of the order of a volt applied between the membrane electrodes would give rise to an electric field of the order of several megavolts per meter in the submicron gap between the electrodes. An electric field of this magnitude would be sufficient to ionize all the molecules that enter the holes. Ionization (but not avalanche arcing) would occur because the distance between the ionizing electrodes would be less than the mean free path of gas molecules at the operating pressure of instrument. An accelerating grid would be located inside the instrument, downstream from the ionizing membrane. The electric potential applied to this grid would be negative relative to the potential on the inside electrode of the ionizing membrane and would be of a magnitude sufficient to generate a moderate electric field. Positive ions leaving the membrane holes would be accelerated in this electric field. The resulting flux of ions away from the ionization membrane would create a partial vacuum that would draw more of the gas medium through the membrane. The figure depicts a filter electrode and detector electrodes located along the sides of a drift tube downstream from the accelerator electrode. These electrodes would apply a transverse AC electric field superimposed on a ramped DC electric field. The AC field would effect differential transverse dispersal of ions. At a given instant of time, the trajectories of most of the ions would be bent toward the electrodes, causing most of the ions to collide with the electrodes and thereby become neutralized. The DC field would partly counteract the dispersive effect of the AC field, straightening the trajectories of a selected species of ions; the selection would vary with the magnitude of the applied DC field. The straightening of the trajectories of the selected ions would enable them to pass into the region between the detector electrodes. Depending on the polarity of the voltage applied to the detector electrodes, the electric field between the detector electrodes would draw the selected ions to one of these electrodes. Hence, the current collected by one of the detector electrodes would be a measure of the abundance of ions of the selected species. The ramping of the filter- electrode DC voltage would sweep the selection of ions through the spectrum of ionic species.
Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter
Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it is a significant contributor for determining signal-to-noise ratios and MS resolution. Here we report on the integration of a 2 GS/s, 14-bit ADC with a structures for lossless ion manipulations (SLIM)-IMS-MS and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided an effective reduction in digitized noise by factor of ~6, owing largely to the use of smaller bit sizes. The low baseline allowed the threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without causing overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a complex mixture of heavy labeled phosphopeptides showed that the 14-bit ADC (compared to the 8-bit ADC) provided a modest signal-to-noise increase (~1.5 to 2-fold) for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernable signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ~14-fold fewer mass spectra to be averaged to produce a mass spectrum with similar S/N as the 8-bit ADC under identical conditions, potentially providing an order of magnitude higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra, and allows a much fuller picture of analyte profiles in complex mixtures to be acquired.
Computational tools and algorithms for ion mobility spectrometry-mass spectrometry
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
Separation of isobaric Amino Acids and Small Molecule Metabolites Using Multipass Ion Mobility Analysis
Amino acids along with small molecule metabolites are important biomarkers for the study and detection of diseases that are initially analyzed in untargeted omics fashion. Amino acids and many metabolites are isomeric, and their specific form can have a significant impact on biological function. Chromatographic separation of isomers is challenging, and they cannot be resolved by mass spectrometry alone. Ion mobility is a technique that allows the separation of ions based on their size, shape, and charge. Here we present the results of the separation of isobaric amino acids and small molecule metabolites using a system that allows for multi-pass ion mobility separation which, in turn, enhances the ion mobility resolution of the separation. Amino acid standards and small molecule metabolites commercially available were infused directly into a SELECT SERIES™ Cyclic™ IMS system. Solutions of individual and mixture of the isobaric species were used and the mobility conditions were optimized for multiple passes for each corresponding set of isobaric species. Both ionization polarities and various solvent adducts were tested to provide the best signal intensity and separation. Amino acids such as leucine and isoleucine have previously been separated with ion mobility in a system with lower ion mobility resolution (SYNAPT™ G2 mass spectrometer) rendering about 90% of valley and mobility resolution of around 40 Ω/ΔΩ. With the enhanced ion mobility resolution using the cyclic IMS technique we have obtained almost complete separation of those amino acids rendering a valley of about 10% after 15 passes. For this case, the mobility resolution is around 250 Ω/ΔΩ. Another example is the separation of glucose-6-phosphate from glucose-1-phosphate, and fructose-6phosphate which were separated after 10 passes. For this case, the mobility resolution is around 205 Ω/ΔΩ.
Exchange, interpretation, and database-search of ion mobility spectra supported by data format JCAMP-DX
To assist peak assignment in ion mobility spectrometry it is important to have quality reference data. The reference collection should be stored in a database system which is capable of being searched using spectral or substance information. We propose to build such a database customized for ion mobility spectra. To start off with it is important to quickly reach a critical mass of data in the collection. We wish to obtain as many spectra combined with their IMS parameters as possible. Spectra suppliers will be rewarded for their participation with access to the database. To make the data exchange between users and system administration possible, it is important to define a file format specially made for the requirements of ion mobility spectra. The format should be computer readable and flexible enough for extensive comments to be included. In this document we propose a data exchange format, and we would like you to give comments on it. For the international data exchange it is important, to have a standard data exchange format. We propose to base the definition of this format on the JCAMP-DX protocol, which was developed for the exchange of infrared spectra. This standard made by the Joint Committee on Atomic and Molecular Physical Data is of a flexible design. The aim of this paper is to adopt JCAMP-DX to the special requirements of ion mobility spectra.