Ion mobility-mass spectrometry: time-dispersive instrumentation

MALDI coupled to modified traveling wave ion mobility mass spectrometry for fast enantiomeric determination

In this work, the use of MALDI traveling wave ion mobility spectrometry-mass spectrometry (MALDI-TWIMS-MS) for stereoselective structural analysis of direct cleavage and identification of 2-substituted piperidines obtained through solid-phase asymmetric synthesis by using heterogeneous 8-phenylmenthyl-based chiral auxiliary resins. A strategy for gas-phase chiral and structural characterization of small molecular weight molecules by using MALDI-IMS-MS technique is discussed. Because both MALDI and IMS do not directly offer chiral resolution, an easy methodology by adding a chiral phase is described to carry out in situ online ion/molecule complexation with different chiral analytes inside the mass spectrometer. Piperidine enantiomers were resolved, and separation obtained shows dependence of surface areas. To corroborate this assumption and elucidate the separation mechanism to accomplish an analytical technique by which fast determination of the chirality of molecules may be determined for a wide range organic compound applications, it was performed DFT calculations to determine the cross-sectional areas of proton-bound dimer complexes. Drift times are affected by cross-sectional areas, correlating bigger times with bigger molecular volumes during the ion mobility experiments of proton-bound dimer complexes.

Molecular Structure Characterization of Riverine and Coastal Dissolved Organic Matter with Ion Mobility Quadrupole Time-of-Flight LCMS (IM Q-TOF LCMS)

Deciphering molecular structures of dissolved organic matter (DOM) components is key to understanding the formation and transformation of this globally important carbon pool in aquatic environments. Such a task depends on the integrated use of complementary analytical techniques. We characterize the molecular structure of natural DOM using an ion mobility quadrupole time of flight liquid chromatography mass spectrometer (IM Q-TOF LC/MS), which provides multidimensional structural information on DOM molecules. Geometric conformation of DOM molecules is introduced into molecular-level analysis via the ion mobility (IM) in the system, and an actual measurement of isomers is achieved for the first time. Our data show that natural DOM molecules from several south Texas rivers and adjacent coastal waters have smaller geometric conformation compared with standard biomolecules. Furthermore, about 10% of all DOM molecules resolved within the detection limit of IM-MS had at least one but no more than four isomers. With acquired geometric and isomeric information, we established a multidimensional database containing 89 natural DOM compounds. This database provides a foundation to expand further, or compare, with DOM data from different seasons and locations.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry

Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed analysis and relative quantification, and provides 3× higher throughput than iTRAQ (isobaric tags for absolute and relative quantification)-4-based methods with high intra- and inter-laboratory reproducibility. The workflow was systematically characterized and benchmarked across three independent laboratories using two distinct breast cancer subtypes from patient-derived xenograft models to enable assessment of proteome and phosphoproteome depth and quantitative reproducibility. Each plex consisted of ten samples, each being 300 μg of peptide derived from <50 mg of wet-weight tissue. Of the 10,000 proteins quantified per sample, we could distinguish 7,700 human proteins derived from tumor cells and 3100 mouse proteins derived from the surrounding stroma and blood. The maximum deviation across replicates and laboratories was <7%, and the inter-laboratory correlation for TMT ratio-based comparison of the two breast cancer subtypes was r > 0.88. The maximum deviation for the phosphoproteome coverage was <24% across laboratories, with an average of >37,000 quantified phosphosites per sample and differential quantification correlations of r > 0.72. The full procedure, including sample processing and data generation, can be completed within 10 d for ten tissue samples, and 100 samples can be analyzed in ~4 months using a single LC-MS/MS instrument. The high quality, depth, and reproducibility of the data obtained both within and across laboratories should enable new biological insights to be obtained from mass spectrometry-based proteomics analyses of cells and tissues together with proteogenomic data integration.

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.

A new retrospective, multi-evidence veterinary drug screening method using drift tube ion mobility mass spectrometry

RATIONALE

The retrospectivity (the ability to retrospect to a previously unknown compound in raw data) is very meaningful for food safety and risk assessment when facing new emerging drugs. Accurate mass and retention time based screening may lead false positive and false negative results so new retrospective, reliable platform is desirable.

METHODS

Different concentration levels of standards with and without matrix were analyzed using ion mobility (IM)-quadrupole-time-of-flight (Q-TOF) for collecting retrospective accurate mass, retention time, drift time and tandem MS evidence for identification in a single experiment. The isomer separation ability of IM and the four-dimensional (4D) feature abundance quantification abilities were evaluated for veterinary drugs for the first time.

RESULTS

The sensitivity of the IM-Q-TOF workflow was obviously higher than that of the traditional database searching algorithm [find by formula (FbF) function] for Q-TOF. In addition, the IM-Q-TOF workflow contained most of the results from FbF and removed the false positive results. Some isomers were separated by IM and the 4D feature abundance quantitation removed interference with similar accurate mass and showed good linearity.

CONCLUSION

A new retrospective, multi-evidence platform was built for veterinary drug screening in a single experiment. The sensitivity was significantly improved and the data can be used for quantification. The platform showed its potential to be used for food safety and risk assessment.

MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals

Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.

Trace analysis by ion mobility spectrometry: From conventional to smart sample preconcentration methods. A review

Ion mobility spectrometry (IMS) is a rapid and high sensitive technique widely used in security and forensic areas. However, a lack of selectivity is usually observed in the analysis of complex samples due to the scarce resolution of the technique. The literature concerning the use of conventional and novel smart materials in the pretreatment and preconcentration of samples previous to IMS determinations has been critically reviewed. The most relevant strategies to enhance selectivity and sensitivity of IMS determinations have been widely discussed, based in the use of smart materials, as immunosorbents, aptamers, molecularly imprinted polymers (MIPs), ionic liquids (ILs) and nanomaterial. The observed trend is focused on the development of IMS analytical methods in combination of selective sample treatments in order to achieve quick, reliable, sensitive, and selective methods for the analysis of complex samples such as biological fluids, food, or environmental samples.

Conformational Landscapes of Ubiquitin, Cytochrome c, and Myoglobin: Uniform Field Ion Mobility Measurements in Helium and Nitrogen Drift Gas

In this study, a commercial uniform field drift tube ion mobility-mass spectrometer (IM-MS) was utilized to measure the gas-phase conformational populations of three well-studied proteins: ubiquitin (8566 Da), cytochrome c (12,359 Da), and myoglobin in both apo and holo forms (16,951 and 17,567 Da, respectively) in order to evaluate the use of this technology for broadscale structural proteomics applications. Proteins were electrosprayed from either acidic organic (pH ~3) or aqueous buffered (pH ~6.6) solution phase conditions, which generated a wide range of cation charge states corresponding to both extended (unfolded) and compact (folded) gas-phase conformational populations. Corresponding collision cross section (CCS) measurements were compiled for significant ion mobility peak features observed at each charge state in order to map the conformational landscapes of these proteins in both helium and nitrogen drift gases. It was observed that the conformational landscapes were similar in both drift gases, with differences being attributed primarily to ion heating during helium operation due to the necessity of operating the instrument with higher pressure differentials. Higher resolving powers were observed in nitrogen, which allowed for slightly better structural resolution of closely-spaced conformer populations. The instrumentation was found to be particularly adept at measuring low abundance conformers which are only present under gentle conditions which minimize ion heating. This work represents the single largest ion mobility CCS survey published to date for these three proteins with 266 CCS values and 117 ion mobility spectra, many of which have not been previously reported.

High performance collision cross section calculation-HPCCS

Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.

Increasing Analytical Separation and Duty Cycle with Nonlinear Analytical Mobility Scan Functions in TIMS-FT-ICR MS

In this work, nonlinear, stepping analytical mobility scan functions are implemented to increase the analytical separation and duty cycle during tandem Trapped Ion Mobility Spectrometry and FT-ICR MS operation. The differences between linear and stepping scan functions are described based on length of analysis, mobility scan rate, signal-to-noise, and mobility resolving power. Results showed that for the linear mobility scan function only a small fraction of the scan is sampled, resulting in the lowest duty cycle 0.5% and longest experiment times. Implementing nonlinear targeted scan functions for analysis of known mobilities resulted in increased duty cycle (0.85%) and resolving powers (R up to 300) with a 6-fold reduction in time from 30 to 5 min. For broad range characterization, a nonlinear mobility stepping scan function provided the best sensitivity, resolving power, duty cycle (4%), and points per peak. The applicability of nonlinear mobility scan functions for the analysis of complex mixtures is illustrated for the case of a direct infusion of a MCF-7 breast cancer cell digest, where isobaric peptides (e.g., DFTPAELR and TTILQSTGK) were separated in the mobility domain (R_IMS: 110) and identified based on their CCS, accurate mass (R_MS: 550k), and tandem MS using IRMPD in the ICR cell.

The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes

Ion-mobility mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.

Broadband ion mobility deconvolution for rapid analysis of complex mixtures

Broadband IM-MS deconvolution allows generation of IM and MS data for species that are UPLC-IM-MS unresolved.

Improving the discovery of secondary metabolite natural products using ion mobility-mass spectrometry

Secondary metabolite discovery requires an unbiased, comprehensive workflow to detect unknown unknowns for which little to no molecular knowledge exists. Untargeted mass spectrometry-based metabolomics is a powerful platform, particularly when coupled with ion mobility for high-throughput gas-phase separations to increase peak capacity and obtain gas-phase structural information. Ion mobility data are described by the amount of time an ion spends in the drift cell, which is directly related to an ion's collision cross section (CCS). The CCS parameter describes the size, shape, and charge of a molecule and can be used to characterize unknown metabolomic species. Here, we describe current and emerging applications of ion mobility-mass spectrometry for prioritization, discovery and structure elucidation, and spatial/temporal characterization.

Multidimensional mass spectrometry characterization of isomeric biodegradable polyesters

The biodegradable polyester copolymer poly(propylene fumarate) (PPF) is increasingly utilized in bone tissue engineering studies due to its suitability as inert cross-linkable scaffold material. The well-defined poly(propylene fumarate) oligomers needed for this purpose are synthesized by post-polymerization isomerization of poly(propylene maleate), which is prepared by ring opening polymerization of maleic anhydride and propylene oxide. In this study, multidimensional mass spectrometry methodologies, interfacing matrix-assisted laser desorption ionization and electrospray ionization with mass analysis, tandem mass spectrometry fragmentation and/or ion mobility mass spectrometry, have been employed to characterize the composition, end groups, chain connectivity and isomeric purity of the isomeric copolyesters poly(propylene maleate)and poly(propylene fumarate). It is demonstrated that the polymerization catalyst is incorporated into the polymer chain (as the initiating chain end) and that the poly(propylene maleate) to poly(propylene fumarate) isomerization using an amine base proceeds with quantitative yield. Hydrolytic degradation is shown not to alter the double bond geometry of the poly(propylene fumarate) or poly(propylene maleate) chains.

Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry?

Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).

Correlating Resolving Power, Resolution, and Collision Cross Section: Unifying Cross-Platform Assessment of Separation Efficiency in Ion Mobility Spectrometry

Here we examine the relationship among resolving power (Rp), resolution (Rpp), and collision cross section (CCS) for compounds analyzed in previous ion mobility (IM) experiments representing a wide variety of instrument platforms and IM techniques. Our previous work indicated these three variables effectively describe and predict separation efficiency for drift tube ion mobility spectrometry experiments. In this work, we seek to determine if our previous findings are a general reflection of IM behavior that can be applied to various instrument platforms and mobility techniques. Results suggest IM distributions are well characterized by a Gaussian model and separation efficiency can be predicted on the basis of the empirical difference in the gas-phase CCS and a CCS-based resolving power definition (CCS/ΔCCS). Notably traveling wave (TWIMS) was found to operate at resolutions substantially higher than a single-peak resolving power suggested. When a CCS-based Rp definition was utilized, TWIMS was found to operate at a resolving power between 40 and 50, confirming the previous observations by Giles and co-workers. After the separation axis (and corresponding resolving power) is converted to cross section space, it is possible to effectively predict separation behavior for all mobility techniques evaluated (i.e., uniform field, trapped ion mobility, traveling wave, cyclic, and overtone instruments) using the equations described in this work. Finally, we are able to establish for the first time that the current state-of-the-art ion mobility separations benchmark at a CCS-based resolving power of >300 that is sufficient to differentiate analyte ions with CCS differences as small as 0.5%.

The potential of Ion Mobility Mass Spectrometry for high-throughput and high-resolution lipidomics

Lipids are a large and highly diverse family of biomolecules, which play essential structural, storage and signalling roles in cells and tissues. Although traditional mass spectrometry (MS) approaches used in lipidomics are highly sensitive and selective, lipid analysis remains challenging due to the chemical diversity of lipid structures, multiple isobaric species and incomplete separation using many forms of chromatography. Ion mobility (IM) separates ions in the gas phase based on their physicochemical properties. Addition of IM to the traditional lipidomic workflow both enhances separation of complex lipid mixtures, beneficial for lipid identification, and improves isomer resolution. Herein, we discuss the recent developments in IM-MS for lipidomics.

Advancing the large-scale CCS database for metabolomics and lipidomics at the machine-learning era

Metabolomics and lipidomics aim to comprehensively measure the dynamic changes of all metabolites and lipids that are present in biological systems. The use of ion mobility-mass spectrometry (IM-MS) for metabolomics and lipidomics has facilitated the separation and the identification of metabolites and lipids in complex biological samples. The collision cross-section (CCS) value derived from IM-MS is a valuable physiochemical property for the unambiguous identification of metabolites and lipids. However, CCS values obtained from experimental measurement and computational modeling are limited available, which significantly restricts the application of IM-MS. In this review, we will discuss the recently developed machine-learning based prediction approach, which could efficiently generate precise CCS databases in a large scale. We will also highlight the applications of CCS databases to support metabolomics and lipidomics.

The potential of ion mobility-mass spectrometry for non-targeted metabolomics

Non-targeted analysis of metabolites in hypothesis-generating workflows has proven its potential to answer essential questions that arise when dealing with complex biological systems. Nevertheless, tracking changes in perturbed systems via accurate quantification and the identification process itself represent the most critical challenges in these workflows. Recent advances in ion mobility-mass spectrometry have enabled this technique to increase the confidence of metabolite annotation by introducing a complementary conditional molecular descriptor, that is collision cross section.

Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy

Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics.

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements

Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (^DTCCS_N2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these ^DTCCS_N2 values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field ^DTCCS_N2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.

LipidCCS: Prediction of Collision Cross-Section Values for Lipids with High Precision To Support Ion Mobility-Mass Spectrometry-Based Lipidomics

The use of collision cross-section (CCS) values derived from ion mobility-mass spectrometry (IM-MS) has been proven to facilitate lipid identifications. Its utility is restricted by the limited availability of CCS values. Recently, the machine-learning algorithm-based prediction (e.g., MetCCS) is reported to generate CCS values in a large-scale. However, the prediction precision is not sufficient to differentiate lipids due to their high structural similarities and subtle differences on CCS values. To address this challenge, we developed a new approach, namely, LipidCCS, to precisely predict lipid CCS values. In LipidCCS, a set of molecular descriptors were optimized using bioinformatic approaches to comprehensively describe the subtle structure differences for lipids. The use of optimized molecular descriptors together with a large set of standard CCS values for lipids (458 in total) to build the prediction model significantly improved the precision. The prediction precision of LipidCCS was externally validated with median relative errors (MRE) of ∼1% using independent data sets across different instruments (Agilent DTIM-MS and Waters TWIM-MS) and laboratories. We also demonstrated that the improved precision in the predicted LipidCCS database (15 646 lipids and 63 434 CCS values in total) could effectively reduce false-positive identifications of lipids. Common users can freely access our LipidCCS web server for the following: (1) the prediction of lipid CCS values directly from SMILES structure; (2) database search; and (3) lipid match and identification. We believe LipidCCS will be a valuable tool to support IM-MS-based lipidomics. The web server is freely available on the Internet ( http://www.metabolomics-shanghai.org/LipidCCS/ ).

Liquid chromatography-high resolution mass spectrometry for the analysis of phytochemicals in vegetal-derived food and beverages

The recent years witnessed a change in the perception of nutrition. Diet does not only provide nutrients to meet the metabolic requirements of the body, but it also constitutes an active way for the consumption of compounds beneficial for human health. Fruit and vegetables are an excellent source of such compounds, thus the growing interest in characterizing phytochemical sources, structures and activities. Given the interest for phytochemicals in food, the development of advanced and suitable analytical techniques for their identification is fundamental for the advancement of food research. In this review, the state of the art of phytochemical research in food plants is described, starting from sample preparation, throughout extract clean-up and compound separation techniques, to the final analysis, considering both qualitative and quantitative investigations. In this regard, from an analytical point of view, fruit and vegetable extracts are complex matrices, which greatly benefit from the use of modern hyphenated techniques, in particular from the combination of high performance liquid chromatography separation and high resolution mass spectrometry, powerful tools which are being increasingly used in the recent years. Therefore, selected applications to real samples are presented and discussed, in particular for the analysis of phenols, polyphenols and phenolic acids. Finally, some hot points are discussed, such as waste characterization for high value-compounds recovery and the untargeted metabolomics approach.

Ion Mobility Spectrometry - High Resolution LTQ-Orbitrap Mass Spectrometry for Analysis of Homemade Explosives

The detailed chemical characterization of homemade explosives (HMEs) and other chemicals that can mimic or mask the presence of explosives is important for understanding and improving the performance of commercial instrumentation used for explosive detection. To that end, an atmospheric-pressure drift tube ion mobility spectrometry (IMS) instrument has been successfully coupled to a commercial tandem mass spectrometry (MS) system. The tandem MS system is comprised of a linear ion trap and a high resolution Orbitrap analyzer. This IMS-MS combination allows extensive characterization of threat chemical compounds, including HMEs, and complex real-world background chemicals that can interfere with detection. Here, the composition of ion species originating from a specific HME, erythritol tetranitrate, has been elucidated using accurate mass measurements, isotopic ratios, and tandem MS. Gated IMS-MS and high-resolution MS have been used to identify minor impurities that can be indicative of the HME source and/or synthesis route. Comparison between data obtained on the IMS/MS system and on commercial stand-alone IMS instruments used as explosive trace detectors (ETDs) has also been performed. Such analysis allows better signature assignments of threat compounds, modified detection algorithms, and improved overall ETD performance. Graphical Abstract ᅟ.

Comparison of Ambient and Atmospheric Pressure Ion Sources for Cystic Fibrosis Exhaled Breath Condensate Ion Mobility-Mass Spectrometry Metabolomics

Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The vast majority of the mortality is due to progressive lung disease. Targeted and untargeted CF breath metabolomics investigations via exhaled breath condensate (EBC) analyses have the potential to expose metabolic alterations associated with CF pathology and aid in assessing the effectiveness of CF therapies. Here, transmission-mode direct analysis in real time traveling wave ion mobility spectrometry time-of-flight mass spectrometry (TM-DART-TWIMS-TOF MS) was tested as a high-throughput alternative to conventional direct infusion (DI) electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) methods, and a critical comparison of the three ionization methods was conducted. EBC was chosen as the noninvasive surrogate for airway sampling over expectorated sputum as EBC can be collected in all CF subjects regardless of age and lung disease severity. When using pooled EBC collected from a healthy control, ESI detected the most metabolites, APCI a log order less, and TM-DART the least. TM-DART-TWIMS-TOF MS was used to profile metabolites in EBC samples from five healthy controls and four CF patients, finding that a panel of three discriminant EBC metabolites, some of which had been previously detected by other methods, differentiated these two classes with excellent cross-validated accuracy. Graphical Abstract ᅟ.

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.

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

Successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development of pregnancy related problems at the molecular level. In this perspective, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.

Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry

Metabolomics and lipidomics aim to profile the wide range of metabolites and lipids that are present in biological samples. Recently, ion mobility spectrometry (IMS) has been used to support metabolomics and lipidomics applications to facilitate the separation and the identification of complex mixtures of analytes. IMS is a gas-phase electrophoretic technique that enables the separation of ions in the gas phase according to their charge, shape and size. Occurring within milliseconds, IMS separation is compatible with modern mass spectrometry (MS) operating with microsecond scan speeds. Thus, the time required for acquiring IMS data does not affect the overall run time of traditional liquid chromatography (LC)-MS-based metabolomics and lipidomics experiments. The addition of IMS to conventional LC-MS-based metabolomics and lipidomics workflows has been shown to enhance peak capacity, spectral clarity and fragmentation specificity. Moreover, by enabling determination of a collision cross-section (CCS) value-a parameter related to the shape of ions-IMS can improve the accuracy of metabolite identification. In this protocol, we describe how to integrate traveling-wave ion mobility spectrometry (TWIMS) into traditional LC-MS-based metabolomic and lipidomic workflows. In particular, we describe procedures for the following: tuning and calibrating a SYNAPT High-Definition MS (HDMS) System (Waters) specifically for metabolomics and lipidomics applications; extracting polar metabolites and lipids from brain samples; setting up appropriate chromatographic conditions; acquiring simultaneously m/z, retention time and CCS values for each analyte; processing and analyzing data using dedicated software solutions, such as Progenesis QI (Nonlinear Dynamics); and, finally, performing metabolite and lipid identification using CCS databases and TWIMS-derived fragmentation information.

Comprehensive characterization of ethoxyquin transformation products in fish feed by traveling-wave ion mobility spectrometry coupled to quadrupole time-of-flight mass spectrometry

Feed additives are typically used in intensive farming production over long periods, and hence, they can accumulate in farmed animal tissues. Concerns regarding the use of ethoxyquin as an antioxidant feed additive, have recently arisen due to its potential conversion into a series of transformation products (TPs). The aim of this work was to characterize the TPs of ethoxyquin in fish feed by a novel approach based on the use of traveling-wave ion mobility spectrometry (TWIMS) coupled to high-resolution quadrupole time-of-flight mass spectrometry (QTOFMS). First, ethoxyquin was oxidized under controlled conditions and the generated TPs were added to a comprehensive database. Atlantic salmon feeds were then screened for ethoxyquin TPs using both targeted and untargeted approaches. Twenty-seven TPs were tentatively identified during the oxidation experiments, fifteen of them also being present in the feed samples. In addition, ten other potential TPs were detected in fish feed following the untargeted approach. Thirty-one of these TPs have been reported for the first time in this work through the oxidation experiments and the feed samples. Therefore, this study provides valuable information on the oxidative fate of ethoxyquin in feed, which can be used for future evaluations of potential risk related to this additive.

Drift tube ion mobility and four-dimensional molecular feature extraction enable data-independent tandem mass spectrometric 'omics' analysis without quadrupole selection

RATIONALE

Quadrupole-based tandem mass spectrometry (MS/MS) plays a critical role in 'omics' studies. However, when a particular m/z precursor is selected by the quadrupole, ions other than the precursor are not transmitted through, and the sensitivity and dynamic range thus diminish. Therefore, separation techniques such as ion mobility (IM) are coupled with MS/MS to improve it.

METHODS

In this workflow, every IM-mass spectrometry (MS) scan was followed by one high-voltage collision energy (CE) scan. The precursors were separated in IM drift time and dissociated after IM; the four-dimensional molecular feature extraction (4D MFE) algorithm was used to align the precursors and their MS/MS spectra based on retention time and drift time distribution. A complicated peptide mixture was selected to exemplify the workflow in a proteomics study.

RESULTS

The new IM-MS-based workflow achieved similar performance in finding proteins compared to the traditional quadrupole-based MS/MS method. However, a significant difference was found between the proteins found by these two methods. For the four concentration levels analyzed, at least 23% more proteins were found by combining the new methods than only using the traditional quadrupole-based MS/MS method.

CONCLUSIONS

The established workflow used the 4D MFE algorithm to analyze a complicated 4D dataset and was demonstrated to find more proteins not found by the traditional quadrupole-based MS/MS method in proteomics application. It is thus an important complementary MS/MS mode for 'omics' studies. Copyright © 2016 John Wiley & Sons, Ltd.

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

Online measurement of photoisomerisation efficiency in solution using ion mobility mass spectrometry

A new method for probing the photoisomerisation of molecules in solution using ion mobility mass spectrometry is described and demonstrated with a azoheteroarene photoswitch.

Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?

Measuring the exposome remains a challenge due to the range and number of anthropogenic molecules that are encountered in our daily lives, as well as the complex systemic responses to these exposures. One option for improving the coverage, dynamic range and throughput of measurements is to incorporate ion mobility spectrometry (IMS) into current MS-based analytical methods. The implementation of IMS in exposomics studies will lead to more frequent observations of previously undetected chemicals and metabolites. LC-IMS-MS will provide increased overall measurement dynamic range, resulting in detections of lower abundance molecules. Alternatively, the throughput of IMS-MS alone will provide the opportunity to analyze many thousands of longitudinal samples over lifetimes of exposure, capturing evidence of transitory accumulations of chemicals or metabolites. The volume of data corresponding to these new chemical observations will almost certainly outpace the generation of reference data to enable their confident identification. In this perspective, we briefly review the state-of-the-art in measuring the exposome, and discuss the potential use for IMS-MS and the physico-chemical property of collisional cross section in both exposure assessment and molecular identification.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.

Investigation of the Complete Suite of the Leucine and Isoleucine Isomers: Toward Prediction of Ion Mobility Separation Capabilities

In this study we investigated 11 isomers with the molecular formula C₆H₁₃NO₂ (m/z 131) to ascertain the potential of utilizing drift tube ion mobility mass spectrometry to aid in the separation of isomeric mixtures. This study of small molecules provides a detailed examination of the application of uniform field ion mobility for a narrow scope of isomers with variations in both bond coordination and stereochemistry. For small molecules, it was observed that in general constitutional isomers are more readily separated by uniform field mobility in comparison to stereoisomers such as enantiomers or diastereomers. Diastereomers exhibited differences in their collision cross section (CCS), but were unresolvable in a mixture, whereas the enantiomers studied did not exhibit statistically different CCS values. A mathematical relationship relating the CCS to resolving power was developed in order to predict the required ion mobility resolving power needed to separate the various isomer classes. For the majority of isomers evaluated in this study, a uniform field-based resolving power of 100 was predicted to be sufficient to resolve over half (∼60%) of all hypothetical isomer pairs, including leucine and isoleucine, whereas their stereoisomers (d- and l-forms) are predicted to be significantly more challenging, if not impossible, to separate by conventional drift tube techniques.