Combined Ion Mobility/Time-of-Flight Mass Spectrometry Study of Electrospray-Generated Ions

Ion Mobility Mass Spectrometry Development and Applications

Although as an analytical method with high specificity and high sensitivity, mass spectrometry (MS) has a wide range of applications in many fields, it still needs other technologies as the assist and supplement to enhance the scope and capability of analysis. Coupling with ion mobility (IM) can make an enhancement effect in the field of pharmaceutical analysis as a supplementary method. The two-dimensional mass technology improves the confidence of compounds annotations while increasing peak capacity, with the gradual deepening of theoretical research on IM-MS, it has shown unique advantages in the complex analysis conditions. IM-MS owns great potential for improving the depth, range, dimension of in-depth drug research. In this review, the principle, instruments and methods, applications, advantages and limitations of IM-MS are described. Here, we also elaborate on the prospects in structural evaluation, separation, and identification of complex compounds for the drug discovery and development phase and the great advantages of macromolecules and omics.

Implementation of Ion Mobility Spectrometry-Based Separations in Structures for Lossless Ion Manipulations (SLIM)

Structures for Lossless Ion Manipulations (SLIM) is a powerful variant of traveling wave ion mobility spectrometry (TW-IMS) that uses a serpentine pattern of microelectrodes deposited onto printed circuit boards to achieve ultralong ion path lengths (13.5 m). Ions are propelled through SLIM platforms via arrays of TW electrodes while RF and DC electrodes provide radial confinement, establishing near lossless transmission. The recent ability to cycle ions multiple times through a SLIM has allowed ion path lengths to exceed 1000 m, providing unprecedented separation power and the ability to observe ion structural conformations unobtainable with other IMS technologies. The combination of high separation power, high signal intensity, and the ability to couple with mass spectrometry places SLIM in the unique position of being able to address longstanding proteomics and metabolomics challenges by allowing the characterization of isomeric mixtures containing low abundance analytes.

Electrospray Ionization Ion Mobility Mass Spectrometry

Electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) is a rapidly progressing analytical technique for the examination of complex compounds in the gas phase. ESI-IMS-MS separates isomers, provides structural information, and quantitatively identifies peptides, lipids, carbohydrates, polymers, and metabolites in biological samples. ESI-IMS-MS has pharmaceutical, environmental, and manufacturing applications quickly characterizing drugs, petroleum products, and metal macromolecules. This review provides the history of ESI-IMS-MS development and applications to date.

Utilizing Drift Tube Ion Mobility Spectrometry for the Evaluation of Metabolites and Xenobiotics

Metabolites and xenobiotics are small molecules with a molecular weight that often falls below 600 Da. Over the last few decades, multiple small molecule databases have been curated listing structures, masses, and fragmentation spectra possible in metabolomic and exposomic measurements. To date only a small portion of the spectra in these databases are experimentally derived due to the high expense of obtaining, synthesizing, and analyzing standards. A vast majority of spectra have thus been created using theoretical programs to fit the available experimental data. The errors associated with theoretical data have however caused problems with current small molecule identifications, and accurate quantitation as searching the databases using just one or two analysis dimensions (i.e., chromatography retention times and mass spectrometry (MS) m/z values) results in numerous annotations for each experimental feature. Additional analysis dimensions are therefore needed to better annotate and identify small molecules. Drift tube ion mobility spectrometry coupled with MS (DTIMS-MS) is a promising technique to address this challenge as it is able to perform rapid structural evaluations of small molecules in complex matrices by assessing the collision cross section values for each in addition to their m/z values. The use of IMS in conjunction with other separation techniques such as gas or liquid chromatography and MS has therefore enabled more accurate identifications for the small molecules present in complex biological and environmental samples. Here, we present a review of relevant parameter considerations for DTIMS application with emphasis on xenobiotics and metabolomics isomer separations.

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples

Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.

Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline's ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. Graphical Abstract ᅟ.

Buffer gas additives (modifiers/shift reagents) in ion mobility spectrometry: Applications, predictions of mobility shifts, and influence of interaction energy and structure

Ion mobility spectrometry (IMS) is an analytical technique used for fast and sensitive detection of illegal substances in customs and airports, diagnosis of diseases through detection of metabolites in breath, fundamental studies in physics and chemistry, space exploration, and many more applications. Ion mobility spectrometry separates ions in the gas-phase drifting under an electric field according to their size to charge ratio. Ion mobility spectrometry disadvantages are false positives that delay transportation, compromise patient's health and other negative issues when IMS is used for detection. To prevent false positives, IMS measures the ion mobilities in 2 different conditions, in pure buffer gas or when shift reagents (SRs) are introduced in this gas, providing 2 different characteristic properties of the ion and increasing the chances of right identification. Mobility shifts with the introduction of SRs in the buffer gas are due to clustering of analyte ions with SRs. Effective SRs are polar volatile compounds with free electron pairs with a tendency to form clusters with the analyte ion. Formation of clusters is favored by formation of stable analyte ion-SR hydrogen bonds, high analytes' proton affinity, and low steric hindrance in the ion charge while stabilization of ion charge by resonance may disfavor it. Inductive effects and the number of adduction sites also affect cluster formation. The prediction of IMS separations of overlapping peaks is important because it simplifies a trial and error procedure. Doping experiments to simplify IMS spectra by changing the ion-analyte reactions forming the so-called alternative reactant ions are not considered in this review and techniques other than drift tube IMS are marginally covered.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Motivation

Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses.

Results

We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software.

Availability and implementation

PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library.

Supplementary information

Supplementary data are available at Bioinformatics online.

Expanding lipidome coverage using MS/MS-aided untargeted data-independent RP-UPLC-TOF-MSE acquisition

Lipid function and importance in disease are being rediscovered due to modern advancements in chemical analysis. RP-UPLC-TOF-MS^E is now the lipidomics tool of choice and can provide the demanded specificity for detecting the great diversity of the lipidome. It can offer simplicity, rapidity, robustness and high throughputness, without the need for further optimization in current sample preparation protocols. This method can cover the major lipid categories with the ability to detect several corresponding subclasses. It can deliver adequate information for deciphering fatty chain length, unsaturation and regioisomerism. It has enabled the detection of a vast number of lipids, of which more than 250 are reported here. These lipids were detected from applications in a variety of biological matrices and species.

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits.

Pulsed Nano-ESI Atmospheric-Pressure Ion Mobility Mass Spectrometry with Enhanced Ion Sampling

Ion mobility-mass spectrometry (IM-MS) has gained considerable attention for detection of clusters and weakly bound species created by electrospray ionization (ESI). Atmospheric-pressure (AP) IM-MS offers an advantage in these studies compared to its low-pressure counterpart, owing to soft introduction of ions into the mobility cell with minimal ion activation. Here, we report new approaches to improve the sensitivity and soft ion introduction in AP-IM-MS. For the former, we demonstrate enhanced aerodynamic sampling of ions from the mobility cell into the MS using pulsed-field sampling. In this approach, ions are driven toward the MS, and the field is shut down once the ions reach the vicinity of the MS inlet orifice. The pulsed-field operation provides arrival times without the need for an exit ion gate in the mobility cell and leads to improvements in sensitivity of up to 1 order of magnitude. For soft ion generation, we report a pulsed nano-ESI source to introduce a packet of ions into the room-temperature mobility cell without induced desolvation. Further, we demonstrate the application of the pulsed nano-ESI AP-IM-MS with enhanced ion sampling for detection of solvent clusters of amines and peptide aggregates.

Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures

Ion mobility is a powerful tool for separating and characterizing the structures of ions. Here, a radio-frequency (rf) confining drift cell is used to evaluate the drift times of ions over a broad range of drift field strengths (E/P, V cm^-1 Torr^-1). The presence of rf potentials radially confines ions and results in excellent ion transmission at low E/P (less than 1 V cm^-1 Torr^-1), thereby reducing the dependence of ion transmission on the applied drift voltage. Non-linear responses between drift time and reciprocal drift voltages are observed for extremely low E/P and high rf amplitudes. Under these conditions, pseudopotential wells generated by the rf potentials dampen the mobility of ions. The effective potential approximation is used to characterize this mobility dampening behavior, which can be mitigated by adjusting rf amplitudes and electrode dimensions. Using SIMION trajectories and statistical arguments, the effective temperatures of ions in an rf-confining drift cell are evaluated. Results for the doubly charged peptide GRGDS suggest that applied rf potentials can result in a subtle increase (2 K) in effective temperature compared to an electrostatic drift tube. Additionally, simulations of native-like ions of the protein complex avidin suggest that rf potentials have a negligible effect on the effective temperature of these ions. In general, the results of this study suggest that applied rf potentials enable the measurement of drift times at extremely low E/P and that these potentials have negligible effects on ion effective temperature. Graphical Abstract ᅟ.

Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry

Mass spectrometry (MS)-based multi-omic measurements, including proteomics, metabolomics, lipidomics, and glycomics, are increasingly transforming our ability to characterize and understand biological systems. Multi-omic analyses and the desire for comprehensive measurement coverage presently have limitations due to the chemical diversity and range of abundances of biomolecules in complex samples. Advances addressing these challenges increasingly are based upon the ability to quickly separate, react and otherwise manipulate sample components for analysis by MS. Here we report on a new approach using Structures for Lossless Ion Manipulations (SLIM) to enable long serpentine path ion mobility spectrometry (IMS) separations followed by MS analyses. This approach provides previously unachieved resolution for biomolecular species, in conjunction with more effective ion utilization, and a basis for greatly improved characterization of very small sample sizes.

Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.

Developing liquid chromatography ion mobility mass spectometry techniques

When a packet of ions in a buffer gas is exposed to a weak electric field, the ions will separate according to differences in their mobilities through the gas. This separation forms the basis of the analytical method known as ion mobility spectroscopy and is highly efficient, in that it can be carried out in a very short time frame (micro- to milliseconds). Recently, efforts have been made to couple the approach with liquid-phase separations and mass spectrometry in order to create a high-throughput and high-coverage approach for analyzing complex mixtures. This article reviews recent work to develop this approach for proteomics analyses. The instrumentation is described briefly. Several multidimensional data sets obtained upon analyzing complex mixtures are shown in order to illustrate the approach as well as provide a view of the limitations and required future work.

Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is a crucial direction for the field of medicine. While MS-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new instrumental platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry separations with liquid chromatography and MS to dramatically increase measurement sensitivity and throughput, further enabling future high throughput MS-based clinical applications. An initial application of the liquid chromatography--ion mobility spectrometry-MS platform analyzing blood serum samples from 60 postliver transplant patients with recurrent fibrosis progression and 60 nontransplant patients illustrates its potential utility for disease characterization.

Continuous flow ion mobility separation with mass spectrometric detection using a nano-radial differential mobility analyzer at low flow rates

We describe a hybrid mass-mobility instrument in which a continuous-flow ion mobility classifier is used as a front-end separation device for mass spectrometric analysis of ions generated with an electrospray ionization source. Using nitrogen as a carrier gas, the resolving power of the nano-radial differential mobility analyzer (nRDMA) for nanometer-sized ions is 5-7 for tetraalkylammonium ions. Data are presented demonstrating the ability of the system to resolve the different aggregation and charge states of tetraalkylammonium ions and protonated peptides using a quadrupole ion trap (QIT) mass spectrometer to analyze the mobility-classified ions. Specifically, data are presented for the two charge states of the decapeptide Gramicidin S. A key feature of the new instrument is the ability to continuously transmit ions with specific mobilities to the mass spectrometer for manipulation and analysis.

Vacuum-integrated electrospray deposition for highly reliable polymer thin film

Vacuum electrospray deposition (ESD) equipment was designed to prepare polymer thin films. The polymer solution can be injected directly into vacuum system through multi-stage pumping line, so that the solvent residues and ambient contaminants are highly reduced. To test the performance of ESD system, we fabricated organic photovoltaic cells (OPVCs) by injecting polymer solution directly onto the substrate inside a high vacuum chamber. The OPVC fabricated has the structure of Al∕P3HT:PCBM∕PEDOT:PSS∕ITO and was optimized by varying the speed of solution injection and concentration of the solution. The power conversion efficiency (PCE) of the optimized OPVC is 3.14% under AM 1.5G irradiation without any buffer layer at the cathode side. To test the advantages of the vacuum ESD, we exposed the device to atmosphere between the deposition steps of the active layer and cathode. This showed that the PCE of the vacuum processed device is 24% higher than that of the air exposed device and confirms the advantages of the vacuum prepared polymer film for high performance devices.

Mass spectrometry for translational proteomics: progress and clinical implications

The utility of mass spectrometry (MS)-based proteomic analyses and their clinical applications have been increasingly recognized over the past decade due to their high sensitivity, specificity and throughput. MS-based proteomic measurements have been used in a wide range of biological and biomedical investigations, including analysis of cellular responses and disease-specific post-translational modifications. These studies greatly enhance our understanding of the complex and dynamic nature of the proteome in biology and disease. Some MS techniques, such as those for targeted analysis, are being successfully applied for biomarker verification, whereas others, including global quantitative analysis (for example, for biomarker discovery), are more challenging and require further development. However, recent technological improvements in sample processing, instrumental platforms, data acquisition approaches and informatics capabilities continue to advance MS-based applications. Improving the detection of significant changes in proteins through these advances shows great promise for the discovery of improved biomarker candidates that can be verified pre-clinically using targeted measurements, and ultimately used in clinical studies - for example, for early disease diagnosis or as targets for drug development and therapeutic intervention. Here, we review the current state of MS-based proteomics with regard to its advantages and current limitations, and we highlight its translational applications in studies of protein biomarkers.

Using high-resolution quadrupole TOF technology in DMPK analyses

Recent advances in quadrupole TOF (Q-TOF) MS have some bioanalytical scientists referring to a ‘paradigm shift’ in their field. They are speaking of a potential move away from workflows based upon triple-quadrupole MS. Gone would be the optimizing of numerous parameters in selected-reaction monitoring (SRM) experiments, replaced with more generic workflows provided by Q-TOF instruments with high data acquisition rates, excellent mass accuracy (≤5 ppm) and high resolving power (≥30,000). Such a move could pay real dividends for high-throughput workflows, especially in drug metabolism and pharmacokinetics analyses where quantitation and qualification studies could actually be merged. But, are modern Q-TOF-MS instruments, touted as high-resolution MS, ready for this? If not, how close is it? This article will examine these questions by reviewing recent advances in Q-TOF technology and some fascinating orthogonal technology (such as ion mobility) that modern Q-TOFs employ for even greater analytical power.

Peptide and protein drug analysis by MS: challenges and opportunities for the discovery environment

Straightforward assay development using MS has become commonplace in most modern pharmaceutical laboratories. In particular, MS is an invaluable tool in the discovery environment of this industry, making it possible to characterize the structures of target drugs and to screen large numbers of potential drug candidates in metabolism and pharmacokinetics studies, and much more. Furthermore, as drug portfolios expand to include biotherapeutic species, such as peptides and proteins, MS is there to meet any analytical challenges. In this article, general aspects of MS in the discovery environment are discussed, as well as what the future might hold.

Chemical standards in ion mobility spectrometry

In ion mobility spectrometry (IMS), reduced mobility values (K(0)) are used as a qualitative measure of gas phase ions, and are reported in the literature as absolute values. Unfortunately, these values do not always match with those collected in the field. One reason for this discrepancy is that the buffer gas may be contaminated with moisture or other volatile compounds. In this study, the effect of moisture and organic contaminants in the buffer gas on the mobility of IMS standards and analytes was investigated for the first time using IMS directly coupled to mass spectrometry. 2,4-Dimethylpyridine, 2,6-di-tert-butylpyridine (DTBP), and tetrabutylammonium, tetrapropylammonium, tetraethylammonium, and tetramethylammonium chlorides were used as chemical standards. In general, the mobility of IMS standard product ions was not affected by small amounts of contamination while the mobilities of many analytes were affected. In the presence of contaminants in the buffer gas, the mobility of analyte ions is often decreased by forming ion-molecule clusters with the contaminant. To ensure the measurement of accurate reduced mobility values, two IMS standards are required: an instrument and a mobility standard. An instrument standard is not affected by contaminants in the buffer gas, and provides an accurate measurement of the instrumental parameters, such as voltage, drift length, pressure, and temperature. The mobility standard behaves like an analyte ion in that the compound's mobility is affected by low levels of contamination in the buffer gas. Prudent use of both of these standards can lead to improved measurement of accurate reduced mobility values.

Deciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies

Detailed knowledge of the tertiary and quaternary structure of proteins and protein complexes is of immense importance in understanding their functionality. Similarly, variations in the conformational states of proteins form the underlying mechanisms behind many biomolecular processes, numerous of which are disease-related. Thus, the availability of reliable and accurate biophysical techniques that can provide detailed information concerning these issues is of paramount importance. Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) offers a unique opportunity to separate multi-component biomolecular entities and to measure the molecular mass and collision cross-section of individual components in a single, rapid (</= 2 min) experiment, providing 3D- architectural information directly. Here we report a method of calibrating a commercially available electrospray ionisation (ESI)-travelling wave ion mobility spectrometry (TWIMS)-mass spectrometer using known cross-sectional areas determined for a range of biomolecules by conventional IMS-MS. Using this method of calibration, we have analysed a range of proteins of differing mass and 3D architecture in their native conformations by ESI-TWIMS-MS and found that the cross-sectional areas measured in this way compare extremely favourably with cross-sectional areas calculated using an in-house computing method based on Protein Data Bank NMR-derived co-ordinates. This not only provides a high degree of confidence in the calibration method, but also suggests that the gas phase ESI- TWIMS-MS measurements relate well to solution-based measurements derived from other biophysical techniques. In order to determine which instrumental parameters affect the ESI-TWIMS-MS cross-sectional area calibration, a systematic study of the parameters used to optimise TWIMS drift time separations has been carried out, observing the effect each parameter has on drift times and IMS resolution. Finally, the ESI-TWIMS-MS cross-sectional area calibration has been applied to the analysis of the amyloidogenic protein beta(2)-microglobulin and measurements for three co-populated conformational families, present under denaturing conditions, have been made: the folded, partially unfolded and unfolded states.

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics

The goal of metabolomics analyses is the detection and quantitation of as many sample components as reasonably possible in order to identify compounds or "features" that can be used to characterize the samples under study. When utilizing electrospray ionization to produce ions for analysis by mass spectrometry (MS), it is important that metabolome sample constituents be efficiently separated prior to ion production, in order to minimize ionization suppression and thereby extend the dynamic range of the measurement, as well as the coverage of the metabolome. Similarly, optimization of the MS inlet and interface can lead to increased measurement sensitivity. This perspective review will focus on the role of high resolution liquid chromatography (LC) separations in conjunction with improved ion production and transmission for LC-MS-based metabolomics. Additional emphasis will be placed on the compromise between metabolome coverage and sample analysis throughput.

Ion mobility mass spectrometry analysis of human glycourinome

Complex carbohydrates are macromolecules biosynthesized in nontemplate-type processes, bearing specific glycoepitopes involved in crucial recognition processes such as cell differentiation and cell-cell interactions. Chemical structure of single components in complex mixtures can be analyzed by mass spectrometry for determination of the size and sequence of monosaccharides involved, branching patterns, and substitution by fucose and sialic acids. For de novo identification of glycoforms in human urinome containing N- and O-free and amino acid-linked oligosaccharides, a novel method of ion mobility tandem mass spectrometry followed by computer-assisted assignment is described. Distinct patterns of ions nested specifically by their m/z values and their drift time are observed by IMS-MS. An additional peak capacity for identification of time-separated m/z values in the IMS TOF MS mode for differentiation of singly, doubly, and triply charged molecular ion species by ion mobility separation contributes to significant reduction of carbohydrate complexity in a given mass window. Profiling of glycoforms from human urinome represents a highly efficient approach for biomarker discovery and differential glycotarget identification, demonstrating potential for diagnosis of human diseases, as for congenital disorders of glycosylation.

Monitoring copopulated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry

The precise mechanism of protein folding remains elusive and there is a deficiency of biophysical techniques that are capable of monitoring the individual behavior of copopulated protein conformers during the folding process. Herein, an ion mobility spectrometry (IMS) device integrated with electrospray ionization mass spectrometry (ESI-MS) has been used to successfully separate and analyze protein conformers differing in cross section and/or charge state. In an initial test, an ensemble of folded and partially folded conformers of the protein cytochrome c was separated. A detailed study undertaken on the amyloidogenic protein beta(2)-microglobulin (beta(2)m), which forms fibrils by protein unfolding followed by self-aggregation and is responsible for the disease dialysis-related amyloidosis, has generated important insights into its folding landscape. Initially, a systematic titration of beta(2)m over the pH range 2 to 7 using ESI-IMS-MS allowed individual conformers to be monitored and quantified throughout the acid denaturation process. Furthermore, a comparison of wild-type beta(2)m with single and double amino acid variants with a range of folding stabilities and propensities for amyloid fibril formation has provided illuminating evidence of the role of different conformers in protein stability and amyloidogenic aggregation. The ESI-IMS-MS data presented here not only demonstrate an important and informative further dimension to ESI-MS, but also illustrate the potential of the ESI-IMS-MS technique for unravelling protein folding enigmas in general and studying protein misfolding diseases in particular.

Distortion of ion structures by field asymmetric waveform ion mobility spectrometry

Field asymmetric waveform ion mobility spectrometry (FAIMS) is emerging as a major analytical tool, especially in conjunction with mass spectrometry (MS), conventional ion mobility spectrometry (IMS), or both. In particular, FAIMS is used to separate protein or peptide conformers prior to characterization by IMS, MS/MS, or H/D exchange. High electric fields in FAIMS induce ion heating, previously estimated at <10 degrees C on average and believed too weak to affect ion geometries. Here we use a FAIMS/IMS/MS system to compare the IMS spectra for ESI-generated ubiquitin ions that have and have not passed FAIMS and find that some unfolding occurs for most charge states. These data and their comparison with the reported protein unfolding in a Paul trap imply that at least some structural transitions observed in FAIMS, or previously in an ion trap, are not spontaneous. The observed unfolding is similar to that produced by heating of approximately 50 degrees C above room temperature, consistent with the calculated heating of ions at FAIMS waveform peaks. Hence, the ion isomerization in FAIMS likely proceeds in steps during the "hot" periods, especially right after entering the device. The process distorts ion geometries and causes ion losses by a "self-cleaning" mechanism and thus should be suppressed as much as possible. We propose achieving that via cooling FAIMS by the amount of ion heating; in most cases, cooling by approximately 75 degrees C should suffice.

Multiplexed ion mobility spectrometry-orthogonal time-of-flight mass spectrometry

Ion mobility spectrometry (IMS) coupled to orthogonal time-of-flight mass spectrometry (TOF) has shown significant promise for the characterization of complex biological mixtures. The enormous complexity of biological samples (e.g., from proteomics) and the need for both biological and technical analysis replicates imposes major challenges for multidimensional separation platforms with regard to both sensitivity and sample throughput. A major potential attraction of the IMS-TOF MS platform is separation speeds exceeding that of conventional condensed-phase separations by orders of magnitude. Known limitations of the IMS-TOF MS platforms that presently mitigate this attraction include the need for extensive signal averaging due to factors that include significant ion losses in the IMS-TOF interface and an ion utilization efficiency of less than approximately 1% with continuous ion sources (e.g., ESI). We have developed a new multiplexed ESI-IMS-TOF mass spectrometer that enables lossless ion transmission through the IMS-TOF as well as a utilization efficiency of >50% for ions from the ESI source. Initial results with a mixture of peptides show a approximately 10-fold increase in signal-to-noise ratio with the multiplexed approach compared to a signal averaging approach, with no reduction in either IMS or TOF MS resolution.

Mechanical ion gate for electrospray-ionization ion-mobility spectrometry

A novel ion gate for electrospray-ionization atmospheric-pressure ion-mobility spectrometry (ESI-IMS) has been constructed and evaluated. The ion gate consisted of a chopper wheel with two windows--one for periodic ion passage from the ESI source into the drift region and the other for timing and synchronization purposes. The instrument contained a 45.0 cm long drift tube comprising 78 stainless steel rings (0.12 cm thick, 4.90 cm o.d., 2.55 cm i.d.). The rings were connected together in series with 3.34-MOmega resistors. The interface plate and the back plate were also connected with the first and the last rings, respectively, of the drift tube with 3.34-MOmega resistors. A potential of -20.0 kV was applied to the back plate and the interface plate was grounded. The drift tube was maintained at an electric field strength of approximately 400 V cm-1. An aperture grid was attached to the last ring in front of a Faraday plate detector, center-to-center. Several sample solutions were electrosprayed at +5.0 kV with +500 V applied to the ion gate. Baseline separations of selected benzodiazepines, antidepressants, and antibiotics were observed with moderate experimental resolution of approximately 70.

Ion mobility spectrometer with radial collisional focusing

An ion mobility spectrometer that has its mobility cell as a 20-segment quadrupole and functionally the q2 of a triple-quadrupole mass spectrometer has been assembled and tested. The combination of high cell pressure (maximum of 4 Torr of helium) and low axial field (20-160 V per 20.2 cm) results in negligible internal excitation of the ions despite applications of rf and axial fields. The presence of collisional focusing ensures efficient ion transmission and good sensitivity. Collision cross sections of atomic, cluster, peptide, and protein ions were measured and found comparable to literature and calculated cross sections.

Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures

Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight (TOF) MS. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions and, hence, the benefit of FAIMS filtering prior to IMS/MS. The effective peak capacities in analyses of tryptic peptides are approximately 500 for FAIMS/IMS separations and approximately 10(6) for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures.

High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces

The utility of ion mobility spectrometry (IMS) for separation of mixtures and structural characterization of ions has been demonstrated extensively, including in biological and nanoscience contexts. A major attraction of IMS is its speed, several orders of magnitude greater than that of condensed-phase separations. Nonetheless, IMS combined with mass spectrometry (MS) has remained a niche technique, substantially because of limited sensitivity resulting from ion losses at the IMS-MS junction. We have developed a new electrospray ionization (ESI)-IMS-QTOF MS instrument that incorporates electrodynamic ion funnels at both front ESI-IMS and rear IMS-QTOF interfaces. The front funnel is of the novel "hourglass" design that efficiently accumulates ions and pulses them into the IMS drift tube. Even for drift tubes of 2-m length, ion transmission through IMS and on to QTOF is essentially lossless across the range of ion masses relevant to most applications. The rf ion focusing at the IMS terminus does not degrade IMS resolving power, which exceeds 100 (for singly charged ions) and is close to the theoretical limit. The overall sensitivity of the present ESI-IMS-MS system is comparable to that of commercial ESI-MS, which should make IMS-MS suitable for analyses of complex mixtures with ultrahigh sensitivity and exceptional throughput.

Modeling the resolution and sensitivity of FAIMS analyses

Field asymmetric waveform ion mobility spectrometry (FAIMS) is rapidly gaining acceptance as a robust, versatile tool for post-ionization separations prior to mass-spectrometric analyses. The separation is based on differences between ion mobilities at high and low electric fields, and proceeds at atmospheric pressure. Two major advantages of FAIMS over condensed-phase separations are its high speed and an ion focusing effect that often improves sensitivity. While selected aspects of FAIMS performance are understood empirically, no physical model rationalizing the resolving power and sensitivity of the method and revealing their dependence on instrumental variables has existed. Here we present a first-principles computational treatment capable of simulating the FAIMS analyzer for virtually any geometry (including the known cylindrical and planar designs) and arbitrary operational parameters. The approach involves propagating an ensemble of ion trajectories through the device in real time under the influence of applied asymmetric potential, diffusional motion incorporating the high-field and anisotropic phenomena, and mutual Coulomb repulsion of ionic charges. Calculations for both resolution and sensitivity are validated by excellent agreement with measurements in different FAIMS modes for ions representing diverse types and analyte classes.

Thermal ionization ion mobility spectrometry of alkali salts

Positive and negative thermal ionization ion mobility spectra (TI-IMS) of some sodium and potassium halides are reported here. The data provide the first measurement of the thermal ionization ion mobility spectrometry of inorganic compounds. A thin Nichrome filament was used as a thermionic ionization source. Sample was directly deposited on the filament, where it was heated and ionized. Each salt produced a different ion mobility pattern, but all sodium salts spectra were common in their first peak. This peak differs from the common peak observed in the spectra of potassium salts. The drift time of the second peak in all spectra was found to be linearly dependent on the size of the counteranion of the salt. Negative thermal ionization ion mobility spectra of alkali halides were also observed. An alkali halide salt (MX), in general, produced its own anion as well as some heavier ions that are thought to be hydrated X- (MX)n species. The capability of the method in quantitative analysis was demonstrated by measuring potassium impurity in sodium bromide. A detection limit of 0.01% K+ in NaBr and a linear rage of 3 orders of magnitude were obtained. The results from this study suggest that TI-IMS has potential as a field technique for the detection of some elements in samples.

Measurement of cluster ions and residue nanoparticles from water samples with an electrospray/differential mobility analyzer

Cluster ions and residue nanoparticles with sizes below 30 nm were generated by electrospraying (ES) and drying droplets of pure water, tap water, and aqueous solutions of salts. The mobility spectra of the cluster ions between 9.1 and 9.3 x 10(-5) m2/(V s) were measured using a differential mobility analyzer (DMA) operated at room temperature and atmospheric pressure. A modified Faraday cup and a condensation nucleus counter were used for detection. The concentrations of total residue/contaminants in the water were determined as a function of sizes of measured aerosol particles and of the initial droplets. Method detection limits were at sub-ppb level for pure water and sub-ppm level for tap water. ES/DMA is capable of simultaneously measuring the mobility distribution of cluster ions and concentration of total residue present in water samples.

Two-dimensional separations with electrospray ionization ambient pressure high-resolution ion mobility spectrometry/quadrupole mass spectrometry

The coupling of ion mobility spectrometry (IMS) instruments with mass spectrometers has been described since early in IMS development, most commonly with quadrupole mass analyzers. The recent development of IMS with time-of-flight (TOF) instruments has demonstrated that the time compatibility (IMS milliseconds and TOFMS microseconds) of the two techniques enables rapid two-dimensional separations to be performed, theoretically in the order of seconds for a complete analysis. This study presents a unique way to operate a traditional IMS/QMS system to attain separations similar to those achieved with IMS/TOF. For this new approach, the quadrupole was slowly scanned in the single-ion monitoring mode while IMS spectra were continually embedded in each m/z step. In this way, two-dimensional separations (IMS drift times and m/z) were obtained using the traditional IMS/QMS arrangement. An example of a five amino acid separation (quadrupole scan of 40 m/z values at a rate of approximately 7 steps/min) led to a complete two-dimensional analysis within 6 min, comparable to rapid chromatographic separations with mass spectrometry. Proposed approaches to reduce the analysis time are discussed and a reduction in the analysis time to less than 1 min is feasible when the IMS/QMS separation conditions are optimized.

Atmospheric pressure ion trapping in a tandem FAIMS-FAIMS coupled to a TOFMS: studies with electrospray generated gramicidin S ions

A tandem FAIMS-FAIMS system for ion trapping at room temperature and atmospheric pressure is described. The first FAIMS device consisted of a side-to-side configuration (sFAIMS) suitable for ion separation, whereas the second FAIMS device was appropriate for ion trapping (tFAIMS). Ions pre-selected by the sFAIMS entered the tFAIMS and were captured by virtual trapping fields at the hemispherical tip of the inner electrode. The use of the sFAIMS, with wider electrode diameters, and consequently better ion separation efficiency than the tFAIMS, lowered the number of background ions captured in the trapping region of tFAIMS, and thus reduced the space charge effects in the trap. This tandem device was coupled to a laboratory built time-of-flight mass spectrometer and was evaluated using the electrospray generated [M + 2H]2+ ion of gramicidin S. The half-time (t1/2) of the exponential decay of the ion cloud in tFAIMS, determined by monitoring the residual intensity of ions extracted from the ion trapping region of tFAIMS after various delay times, was about 2 s.

Coulomb fission event resolved progeny droplet production from isolated evaporating methanol droplets

An electrodynamic balance was used to levitate a single methanol droplet while it evaporated down to, and just beyond, its first encountered Coulomb fission limit as ascertained by the time dependence of its laser light scatter signal. At its Coulomb limit, the primary droplet fragmented and approximately 81% of its net charge was released in the form of small droplets that are termed progeny. The window of time over which the progeny droplets were ejected from the electrodynamic balance was deltat = 850 ms, indicating that these droplets were formed with a range of mass-to-charge values. An average of 13.2 (+/-4.4) progeny droplets were detected as a result of this fragmentation event. On the assumption that the average initial radius of the progeny droplets were one-tenth the radius of the droplet undergoing the Coulomb fission event, approximately 50% of the total net charge ejected would not have been carried by the 13 progeny droplets detected.

Elongated conformers of charge states +11 to +15 of bovine ubiquitin studied using ESI-FAIMS-MS

Recent advancements in high-field asymmetric waveform ion mobility spectrometry (FAIMS) have led to significant improvements in the application of this technology to the study of protein conformers. Compared with previous work, the maximum value of the separation voltage (i.e., the dispersion voltage) has increased, thereby enabling multiple, elongated conformers of individual charge states of bovine ubiquitin to be separated in the gas phase (e.g., four conformers of each of the +11 and +12 charge states were separated). The use of a carrier gas mixture of 40% nitrogen and 60% helium changed the separation selectivity compared with pure nitrogen and enhanced the signal intensity, especially for the +14 and +15 charge states (the latter was not detected in a nitrogen carrier gas). Conformer cross sections were determined using the FAIMS/energy-loss method and found to be similar within a given charge state. The cross sections for conformers of charge states +13, + 14, and +15 plateau at about 2000 A2 suggesting that the structure of bovine ubiquitin is essentially unfolded after the addition of the 13th proton.

Ion trap/ion mobility/quadrupole/time-of-flight mass spectrometry for peptide mixture analysis

An ion trap/ion mobility/quadrupole/time-of-flight mass spectrometer has been developed for the analysis of peptide mixtures. In this approach, a mixture of peptides is electrosprayed into the gas phase. The mixture of ions that is created is accumulated in an ion trap and periodically injected into a drift tube where ions separate according to differences in gas-phase ion mobilities. Upon exiting the drift tube, ions enter a quadrupole mass filter where a specific mass-to-charge (m/z) ratio can be selected prior to collisional activation in an octopole collision cell. Parent and fragment ions that exit the collision cell are analyzed using a reflectron geometry time-of-flight mass spectrometer. The overall configuration allows different species to be selected according to their mobilities and m/z ratios prior to collision-induced dissociation and final MS analysis. A key parameter in these studies is the pressure of the target gas in the collision cell. Above a critical pressure, the well-defined mobility separation degrades. The approach is demonstrated by examining a mixture of tryptic digest peptides of ubiquitin.