Ion Mobility Collision Cross Section Compendium

Setting the Separation Factor α for Ketone Monomers and Dimers by the Use of Different Drift Gases

This study investigates the influence of different drift gases on ion mobility in ion mobility spectrometry (IMS) using ketones as model substances within a custom-built drift tube spectrometer. Different binary mixtures of nitrogen, helium, and argon were used as drift gases to investigate the influence of mobility on the monomers and dimers of the different ketones. Experimental results reveal shifts in ion drift times and separation factors (α) with varying gas compositions, in accordance with Blanc's Law. Furthermore, the study underscores the device-independent nature of α and the device-dependent resolution, emphasizing the importance of comparative analyses. Employing 2-hexanone and 2-decanone in the same sample but with different drift gases is used to show the impact of different drift gases. By changing the drift gas composition, total alignment of drift times and therefore no possible resolution or baseline resolution could be achieved. Through different experiments and analyses, this research provides insights into the interactions between gas composition and ion mobility, offering implications for diverse analytical applications from environmental monitoring to chemical detection.

High-resolution ion mobility based on traveling wave structures for lossless ion manipulation resolves hidden lipid features

High-resolution ion mobility (resolving power > 200) coupled with mass spectrometry (MS) is a powerful analytical tool for resolving isobars and isomers in complex samples. High-resolution ion mobility is capable of discerning additional structurally distinct features, which are not observed with conventional resolving power ion mobility (IM, resolving power ~ 50) techniques such as traveling wave IM and drift tube ion mobility (DTIM). DTIM in particular is considered to be the "gold standard" IM technique since collision cross section (CCS) values are directly obtained through a first-principles relationship, whereas traveling wave IM techniques require an additional calibration strategy to determine accurate CCS values. In this study, we aim to evaluate the separation capabilities of a traveling wave ion mobility structures for lossless ion manipulation platform integrated with mass spectrometry analysis (SLIM IM-MS) for both lipid isomer standards and complex lipid samples. A cross-platform investigation of seven subclass-specific lipid extracts examined by both DTIM-MS and SLIM IM-MS showed additional features were observed for all lipid extracts when examined under high resolving power IM conditions, with the number of CCS-aligned features that resolve into additional peaks from DTIM-MS to SLIM IM-MS analysis varying between 5 and 50%, depending on the specific lipid sub-class investigated. Lipid CCS values are obtained from SLIM IM (TW(SLIM)CCS) through a two-step calibration procedure to align these measurements to within 2% average bias to reference values obtained via DTIM (DTCCS). A total of 225 lipid features from seven lipid extracts are subsequently identified in the high resolving power IM analysis by a combination of accurate mass-to-charge, CCS, retention time, and linear mobility-mass correlations to curate a high-resolution IM lipid structural atlas. These results emphasize the high isomeric complexity present in lipidomic samples and underscore the need for multiple analytical stages of separation operated at high resolution.

Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.

Interplatform comparison between three ion mobility techniques for human plasma lipid collision cross sections

The implementation of ion mobility spectrometry (IMS) in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) workflows has become a valuable tool for improving compound annotation in metabolomics analyses by increasing peak capacity and by adding a new molecular descriptor, the collision cross section (CCS). Although some studies reported high repeatability and reproducibility of CCS determination and only few studies reported good interplatform agreement for small molecules, standardized protocols are still missing due to the lack of reference CCS values and reference materials. We present a comparison of CCS values of approximatively one hundred lipid species either commercially available or extracted from human plasma. We used three different commercial ion mobility technologies from different laboratories, drift tube IMS (DTIMS), travelling wave IMS (TWIMS) and trapped IMS (TIMS), to evaluate both instrument repeatability and interlaboratory reproducibility. We showed that CCS discrepancies of 0.3% (average) could occur depending on the data processing software tools. Moreover, eleven CCS calibrants were evaluated yielding mean RSD below 2% for eight calibrants, ESI Low concentration tuning mix (Tune Mix) showing the lowest RSD (< 0.5%) in both ion modes. Tune Mix calibrated CCS from the three different IMS instruments proved to be well correlated and highly reproducible (R2 > 0.995 and mean RSD ≤ 1%). More than 90% of the lipid CCS had deviations of less than 1%, demonstrating high comparability between techniques, and the possibility to use the CCS as molecular descriptor. We highlighted the need of standardized procedures for calibration, data acquisition, and data processing. This work demonstrates that using harmonized analytical conditions are required for interplatform reproducibility for CCS determination of human plasma lipids.

Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry

Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.

Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method using ultrahigh-performance liquid chromatography (UPLC) coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples. The experimental CCS values, along with mass spectral properties, were reported for the 174 metabolites. The experimental data included the mass-to-charge ratio (m/z), retention time (RT), tandem MS (MS/MS) spectra, and CCS values. Among the studied metabolites, 263 traveling wave ion mobility spectrometry (TWIMS)-derived CCS values (TWCCSN2) were reported for the first time, and more than 70% of these were CCS values of VLMs. The TWCCSN2 values were highly repeatable, with inter-day variations of <1% relative standard deviation (RSD). The developed method revealed excellent TWCCSN2 accuracy with a CCS difference (ΔCCS) within ±2% of the reported drift tube IMS (DTIMS) and TWIMS CCS values. The complexity of the urine matrix did not affect the precision of the method, as evidenced by ΔCCS within ±1.92%. According to the Metabolomics Standards Initiative, 55 urinary metabolites were identified with a confidence level of 1. Among these 55 metabolites, 53 (96%) were VLMs. The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values, which clearly increased metabolite identification confidence.

Ion Mobility Mass Spectrometry for Large Synthetic Molecules: Expanding the Analytical Toolbox

Understanding the composition, structure and stability of larger synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not always provide this information. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, complementary techniques and computational methods, can be used to structurally characterize synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, nanoclusters, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes.

Mass Spectrometry Investigation of Some ATP-Binding Cassette (ABC) Proteins

Drug resistance remains one of the main causes of poor outcome in cancer therapy. It is also becoming evident that drug resistance to both chemotherapy and to antibiotics is driven by more than one mechanism. So far, there are at least eight recognized mechanisms behind such resistance. In this review, we choose to discuss one of these mechanisms, which is known to be partially driven by a class of transmembrane proteins known as ATP-binding cassette (ABC) transporters. In normal tissues, ABC transporters protect the cells from the toxic effects of xenobiotics, whereas in tumor cells, they reduce the intracellular concentrations of anticancer drugs, which ultimately leads to the emergence of multidrug resistance (MDR). A deeper understanding of the structures and the biology of these proteins is central to current efforts to circumvent resistance to both chemotherapy, targeted therapy, and antibiotics. Understanding the biology and the function of these proteins requires detailed structural and conformational information for this class of membrane proteins. For many years, such structural information has been mainly provided by X-ray crystallography and cryo-electron microscopy. More recently, mass spectrometry-based methods assumed an important role in the area of structural and conformational characterization of this class of proteins. The contribution of this technique to structural biology has been enhanced by its combination with liquid chromatography and ion mobility, as well as more refined labelling protocols and the use of more efficient fragmentation methods, which allow the detection and localization of labile post-translational modifications. In this review, we discuss the contribution of mass spectrometry to efforts to characterize some members of the ATP-binding cassette (ABC) proteins and why such a contribution is relevant to efforts to clarify the link between the overexpression of these proteins and the most widespread mechanism of chemoresistance.

MOCCal: A Multiomic CCS Calibrator for Traveling Wave Ion Mobility Mass Spectrometry

Ion mobility mass spectrometry (IM-MS) is a rapid, gas-phase separation technology that can resolve ions on the basis of their size-to-charge and mass-to-charge ratios. Since each class of biomolecule has a unique relationship between size and mass, IM-MS spectra of complex biological samples are organized into trendlines that each contain one type of biomolecule (i.e., lipid, peptide, metabolite). These trendlines can aid in the identification of unknown ions by providing a general classification, while more specific identifications require the conversion of IM arrival times to collision cross section (CCS) values to minimize instrument-to-instrument variability. However, the process of converting IM arrival times to CCS values varies between the different IM devices. Arrival times from traveling wave ion mobility (TWIM) devices must undergo a calibration process to obtain CCS values, which can impart biases if the calibrants are not structurally similar to the analytes. For multiomic mixtures, several different types of calibrants must be used to obtain the most accurate CCS values from TWIM platforms. Here we describe the development of a multiomic CCS calibration tool, MOCCal, to automate the assignment of unknown features to the power law calibration that provides the most accurate CCS value. MOCCal calibrates every experimental arrival time with up to three class-specific calibration curves and uses the difference (in Å2) between the calibrated TWCCSN2 value and DTCCSN2 vs m/z regression lines to determine the best calibration curve. Using real and simulated multiomic samples, we demonstrate that MOCCal provides accurately calibrated TWCCSN2 values for small molecules, lipids, and peptides.

Suspect and nontarget screening of per- and polyfluoroalkyl substances based on ion mobility mass spectrometry and machine learning techniques

High-resolution mass spectrometry (HRMS)-based suspect and nontarget screening techniques are powerful tools for the comprehensive identification of per- and polyfluoroalkyl substances (PFASs), but the interference of complex matrices (especially for wastewater) pose an analytical challenge. This study explored the potential of combining ion mobility spectrometry (IMS) with HRMS and machine learning techniques to achieve the rapid and accurate suspect and nontarget screening of PFAS in wastewater. There were fewer interfering peaks and a clearer spectrum in the data acquired by IMS-HRMS than conventional HRMS. The introduction of collision cross section (CCS) in PFAS homologous series search could filter out 63% of false positive results. Retention time and CCS prediction models were helpful in improving the confidence for PFAS qualitative identification and the random forest algorithm combined with RDKit descriptor performed best for CCS prediction. With the inclusion of extra dimensional information, this study also proposed a comprehensive and concise confidence assignment criterion to better convey the certainty of the qualitative identification of PFAS. Finally, a total of 56 potential PFASs were identified in the wastewater sample using the newly developed method and 45 of them were identified outside reference standards, emphasizing the importance of suspect and nontarget screening for PFAS.

Application of Ion Mobility Spectrometry and the Derived Collision Cross Section in the Analysis of Environmental Organic Micropollutants

Ion mobility spectrometry (IMS) is a rapid gas-phase separation technique, which can distinguish ions on the basis of their size, shape, and charge. The IMS-derived collision cross section (CCS) can serve as additional identification evidence for the screening of environmental organic micropollutants (OMPs). In this work, we summarize the published experimental CCS values of environmental OMPs, introduce the current CCS prediction tools, summarize the use of IMS and CCS in the analysis of environmental OMPs, and finally discussed the benefits of IMS and CCS in environmental analysis. An up-to-date CCS compendium for environmental contaminants was produced by combining CCS databases and data sets of particular types of environmental OMPs, including pesticides, drugs, mycotoxins, steroids, plastic additives, per- and polyfluoroalkyl substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs), as well as their well-known transformation products. A total of 9407 experimental CCS values from 4170 OMPs were retrieved from 23 publications, which contain both drift tube CCS in nitrogen (DTCCSN2) and traveling wave CCS in nitrogen (TWCCSN2). A selection of publicly accessible and in-house CCS prediction tools were also investigated; the chemical space covered by the training set and the quality of CCS measurements seem to be vital factors affecting the CCS prediction accuracy. Then, the applications of IMS and the derived CCS in the screening of various OMPs were summarized, and the benefits of IMS and CCS, including increased peak capacity, the elimination of interfering ions, the separation of isomers, and the reduction of false positives and false negatives, were discussed in detail. With the improvement of the resolving power of IMS and enhancements of experimental CCS databases, the practicability of IMS in the analysis of environmental OMPs will continue to improve.

Integration of non-targeted multicomponent profiling, targeted characteristic chromatograms and quantitative to accomplish systematic quality evaluation strategy of Huo-Xiang-Zheng-Qi oral liquid

Huo-Xiang-Zheng-Qi oral liquid (HXZQOL) is a well-known traditional Chinese medicine formula for the treatment of gastrointestinal diseases, with the pharmacologic effects of antiinflammatory, immune protection and gastrointestinal motility regulation. More significantly, HXZQOL is recommended for the treatment of COVID-19 patients with gastrointestinal symptoms, and it has been clinically proven to reduce the inflammatory response in patients with COVID-19. However, the effective and overall quality control of HXZQOL is currently limited due to its complex composition, especially the large amount of volatile and non-volatile active components involved. In this study, aimed to fully develop a comprehensive strategy based on non-targeted multicomponent identification, targeted authentication and quantitative analysis for quality evaluation of HXZQOL from different batches. Firstly, the non-targeted high-definition MSE (HDMSE) approach is established based on UHPLC/IM-QTOF-MS, utilized for multicomponent comprehensive characterization of HXZQOL. Combined with in house library-driven automated peak annotation and comparison of 47 reference compounds, 195 components were initially identified. In addition, HS-SPME-GC-MS was employed to analyze the volatile organic compounds (VOCs) in HXZQOL, and a total of 61 components were identified by comparison to the NIST database, reference compounds as well as retention indices. Secondly, based on the selective ion monitoring (SIM) of 24 "identity markers" (involving each herbal medicine), characteristic chromatograms (CCs) were established on LC-MS and GC-MS respectively, to authenticate 15 batches of HXZQOL samples. The targeted-SIM CCs showed that all marker compounds in 15 batches of samples could be accurately monitored, which could indicate preparations authenticity. Finally, a parallel reaction monitoring (PRM) method was established and validated to quantify the nine compounds in 15 batches of HXZQOL. Conclusively, this study first reports chemical-material basis, SIM CCs and quality evaluation of HXZQOL, which is of great implication to quality control and ensuring the authenticity of the preparation.

Improving LC-MS/MS measurements of steroids with differential mobility spectrometry

Introduction

Steroid measurements are important for diagnosis and monitoring of many conditions and treatment regiments; however, due to structural and chemical similarities amongst steroids, these analyses are challenging, even for highly specific techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differential mobility spectrometry (DMS) has the potential to improve these analyses by providing an orthogonal and complementary separation technique.

Methods

Initially, the potential for DMS to improve signal-to-noise ratio (S/N) and reduce interference was tested by comparing chromatograms acquired with and without DMS when performing measurements of six different steroids. Subsequently, a full clinical validation of cortisol and cortisone in urine was performed with the LC-DMS-MS/MS method.

Results and Discussion

DMS significantly reduced interferences observed in the chromatograms and boosted S/N by between 1.6 and 13.8 times. Additionally, DMS improved the agreement between quantifier/qualifier fragment ion results for cortisol and cortisone as indicated by the increase in R2 from approximately 0.81 to 0.98. All validation studies met acceptance criteria and we observed exceptional analytical performance in terms of precision, with % CVs less than 8%.

Conclusions

DMS improved the specificity of the steroid measurements by reducing interferences and improving S/N. The validation studies prove that these benefits did not come at the expense of other aspects of analytical performance. This study indicates that DMS has the potential to benefit not just clinical measurements of challenging analytes, but many clinical LC-MS/MS analyses.

AllCCS2: Curation of Ion Mobility Collision Cross-Section Atlas for Small Molecules Using Comprehensive Molecular Representations

The development of ion mobility-mass spectrometry (IM-MS) has revolutionized the analysis of small molecules, such as metabolomics, lipidomics, and exposome studies. The curation of comprehensive reference collision cross-section (CCS) databases plays a pivotal role in the successful application of IM-MS for small-molecule analysis. In this study, we presented AllCCS2, an enhanced version of AllCCS, designed for the universal prediction of the ion mobility CCS values of small molecules. AllCCS2 incorporated newly available experimental CCS data, including 10,384 records and 7713 unified values, as training data. By leveraging a neural network trained on diverse molecular representations encompassing mass spectrometry features, molecular descriptors, and graph features extracted using a graph convolutional network, AllCCS2 achieved exceptional prediction accuracy. AllCCS2 achieved median relative error (MedRE) values of 0.31, 0.72, and 1.64% in the training, validation, and testing sets, respectively, surpassing existing CCS prediction tools in terms of accuracy and coverage. Furthermore, AllCCS2 exhibited excellent compatibility with different instrument platforms (DTIMS, TWIMS, and TIMS). The prediction uncertainties in AllCCS2 from the training data and the prediction model were comprehensively investigated by using representative structure similarity and model prediction variation. Notably, small molecules with high structural similarities to the training set and lower model prediction variation exhibited improved accuracy and lower relative errors. In summary, AllCCS2 serves as a valuable resource to support applications of IM-MS technologies. The AllCCS2 database and tools are freely accessible at http://allccs.zhulab.cn/.

Permethylation and Metal Adduction: A Toolbox for the Improved Characterization of Glycolipids with Cyclic Ion Mobility Separations Coupled to Mass Spectrometry

Lipids are an important class of molecules involved in various biological functions but remain difficult to characterize through mass-spectrometry-based methods because of their many possible isomers. Glycolipids, specifically, play important roles in cell signaling but display an even greater level of isomeric heterogeneity as compared to other lipid classes stemming from the introduction of a carbohydrate and its corresponding linkage position and α/β anomericity at the headgroup. While liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidomics, it is still unable to characterize all isomeric species, thus presenting the need for new, orthogonal, methodologies. Ion mobility spectrometry-mass spectrometry (IMS-MS) can provide an additional dimension of information that supplements LC-MS/MS workflows, but has seen little use for glycolipid analyses. Herein, we present an analytical toolbox that enables the characterization of various glycolipid isomer sets using high-resolution cyclic ion mobility separations coupled with mass spectrometry (cIMS-MS). Specifically, we utilized a combination of both permethylation and metal adduction to fully resolve isomeric sphingolipids and ceramides with our cIMS-MS platform. We also introduce a new metric that can enable comparing peak-to-peak resolution across varying cIMS-MS pathlengths. Overall, we envision that our presented methodologies are highly amenable to existing LC-MS/MS-based workflows and can also have broad utility toward other omics-based analyses.

Collision cross section measurement and prediction methods in omics

Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.

Development of a Rapid, Targeted LC-IM-MS Method for Anabolic Steroids

Anabolic steroids are of high biological interest due to their involvement in human development and disease progression. Additionally, they are banned in sport due to their performance-enhancing characteristics. Analytical challenges associated with their measurement stem from structural heterogeneity, poor ionization efficiency, and low natural abundance. Their importance in a variety of clinically relevant assays has prompted the consideration of integrating ion mobility spectrometry (IMS) into existing LC-MS assays, due primarily to its speed and structure-based separation capability. Herein we have optimized a rapid (2 min) targeted LC-IM-MS method for the detection and quantification of 40 anabolic steroids and their metabolites. First, a steroid-specific calibrant mixture was developed to cover the full range of retention time, mobility, and accurate mass. Importantly, this use of this calibrant mixture provided robust and reproducible measurements based on collision cross section (CCS) with interday reproducibility of <0.5%. Furthermore, the combined separation power of LC coupled to IM provided comprehensive differentiation of isomers/isobars within 6 different isobaric groups. Multiplexed IM acquisition also provided improved limits of detection, which were well below 1 ng/mL in almost all compounds measured. This method was also capable of steroid profiling, providing quantitative ratios (e.g., testosterone/epitestosterone, androsterone/etiocholanolone, etc.). Lastly, phase II steroid metabolites were probed in lieu of hydrolysis to demonstrate the ability to separate those analytes and provide information beyond total steroid concentration. This method has tremendous potential for rapid analysis of steroid profiles in human urine spanning a variety of applications from developmental disorders to doping in sport.

MobCal-MPI 2.0: an accurate and parallelized package for calculating field-dependent collision cross sections and ion mobilities

Ion mobility spectrometry (IMS), which can be employed as either a stand-alone instrument or coupled to mass spectrometry, has become an important tool for analytical chemistry. Because of the direct relation between an ion's mobility and its structure, which is intrinsically related to its collision cross section (CCS), IMS techniques can be used in tandem with computational tools to elucidate ion geometric structure. Here, we present MobCal-MPI 2.0, a software package that demonstrates excellent accuracy (RMSE 2.16%) and efficiency in calculating low-field CCSs via the trajectory method (≤30 minutes on 8 cores for ions with ≤70 atoms). MobCal-MPI 2.0 expands on its predecessor by enabling the calculation of high-field mobilities through the implementation of the 2^nd order approximation to two-temperature theory (2TT). By further introducing an empirical correction to account for deviations between 2TT and experiment, MobCal-MPI 2.0 can compute accurate high-field mobilities that exhibit a mean deviation of <4% from experimentally measured values. Moreover, the velocities used to sample ion-neutral collisions were updated from a weighted to a linear grid, enabling the near-instantaneous evaluation of mobility/CCS at any effective temperature from a single set of N₂ scattering trajectories. Several enhancements made to the code are also discussed, including updates to the statistical analysis of collision event sampling and benchmarking of overall performance.

Highly Efficient Ion Manipulator for Tandem Ion Mobility Spectrometry: Exploring a Versatile Technique by a Study of Primary Alcohols

In this work, we present a tandem ion mobility spectrometer (IMS) utilizing a highly efficient ion manipulator allowing to store, manipulate, and analyze ions under high electric field strengths and controlled ion-neutral reactions at ambient conditions. The arrangement of tandem drift regions and an ion manipulator in a single drift tube allows a sequence of mobility selection of precursor ions, followed by storage and analysis, mobility separation, and detection of the resulting product ions. In this article, we present a journey exploring the capabilities of the present instrument by a study of eight different primary alcohols characterized at reduced electric field strengths E/N of up to 120 Td with a water vapor concentration ranging from 40 to 540 ppb. Under these conditions, protonated alcohol monomers up to a carbon number of nine could be dissociated, resulting in 18 different fragmented product ions in total. The fragmentation patterns revealed regularities, which can be used for assignment to the chemical class and improved classification of unknown substances. Furthermore, both the time spent in high electrical field strengths and the reaction time with water vapor can be tuned precisely, allowing the fragment distribution to be influenced. Thus, further information regarding the relations of the product ions can be gathered in a standalone drift tube IMS for the first time.

A Comparison of the Performance of Modular Standalone Do-It-Yourself Ion Mobility Spectrometry Systems

As the spectrum of ion mobility spectrometry (IMS) applications expands and more experimental configurations are developed, identifying the correct platform for an experimental campaign becomes more challenging for researchers. Additionally, metrics that compare performance (Rp, for example) often have nuanced differences in definition between platforms that render direct comparisons difficult. Here we present a comparison of three do-it-yourself (DIY) drift tubes that are relatively low cost and easy to construct, where the performance of each is evaluated based on three different metrics: resolving power, the ideality of resolving powers, and accuracy/precision of K0 values. The standard PCBIMS design developed by Reinecke and Clowers (Reinecke, T.; Clowers, B. H. HardwareX 2018, 4, e00030) provided the highest resolving power (>90) and the highest ideality of resolving power ratios (>90% at best) of the three systems. However, the flexible tube (FlexIMS) construction as described by Smith et al. (Smith, B. L. Anal. Chem. 2020, 92 (13), 9104-9112) exhibited the highest degree of precision of K0 values (relative standard deviation of <0.42%). Depending on the application, the drift tube variants presented and evaluated here offer a low-cost alternative to commercial drift-tube systems with levels of performance that approach theoretical maxima.

A mass spectrum-oriented computational method for ion mobility-resolved untargeted metabolomics

Ion mobility (IM) adds a new dimension to liquid chromatography-mass spectrometry-based untargeted metabolomics which significantly enhances coverage, sensitivity, and resolving power for analyzing the metabolome, particularly metabolite isomers. However, the high dimensionality of IM-resolved metabolomics data presents a great challenge to data processing, restricting its widespread applications. Here, we develop a mass spectrum-oriented bottom-up assembly algorithm for IM-resolved metabolomics that utilizes mass spectra to assemble four-dimensional peaks in a reverse order of multidimensional separation. We further develop the end-to-end computational framework Met4DX for peak detection, quantification and identification of metabolites in IM-resolved metabolomics. Benchmarking and validation of Met4DX demonstrates superior performance compared to existing tools with regard to coverage, sensitivity, peak fidelity and quantification precision. Importantly, Met4DX successfully detects and differentiates co-eluted metabolite isomers with small differences in the chromatographic and IM dimensions. Together, Met4DX advances metabolite discovery in biological organisms by deciphering the complex 4D metabolomics data.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations

BACKGROUND

Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques.

AIM OF REVIEW

In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.

Different ion mobility-mass spectrometry coupling techniques to promote metabolomics

Metabolomics has become increasingly popular in recent years for many applications ranging from clinical diagnosis, human health to biotechnological questioning. Despite technological advances, metabolomic studies are still currently limited by the difficulty of identifying all metabolites, a class of compounds with great chemical diversity. Although lengthy chromatographic analyses are often used to obtain comprehensive data, many isobar and isomer metabolites still remain unresolved, which is a critical point for the compound identification. Currently, ion mobility spectrometry is being explored in metabolomics as a way to improve metabolome coverage, analysis throughput and isomer separation. In this review, all the steps of a typical workflow for untargeted metabolomics are discussed considering the use of an ion mobility instrument. An overview of metabolomics is first presented followed by a brief description of ion mobility instrumentation. The ion mobility potential for complex mixture analysis is discussed regarding its coupling with a mass spectrometer alone, providing gas-phase separation before mass analysis as well as its combination with different separation platforms (conventional hyphenation but also multidimensional ion mobility couplings), offering multidimensional separation. Various instrumental and analytical conditions for improving the ion mobility separation are also described. Finally, data mining, including software packages and visualization approaches, as well as the construction of ion mobility databases for the metabolite identification are examined.

Collision Cross-Section Calibration Strategy for Lipid Measurements in SLIM-Based High-Resolution Ion Mobility

Structures for lossless ion manipulation-based high-resolution ion mobility (HRIM) interfaced with mass spectrometry has emerged as a powerful tool for the separation and analysis of many isomeric systems. IM-derived collision cross section (CCS) is increasingly used as a molecular descriptor for structural analysis and feature annotation, but there are few studies on the calibration of CCS from HRIM measurements. Here, we examine the accuracy, reproducibility, and practical applicability of CCS calibration strategies for a broad range of lipid subclasses and develop a straightforward and generalizable framework for obtaining high-resolution CCS values. We explore the utility of using structurally similar custom calibrant sets as well as lipid subclass-specific empirically derived correction factors. While the lipid calibrant sets lowered overall bias of reference CCS values from ∼2-3% to ∼0.5%, application of the subclass-specific correction to values calibrated with a broadly available general calibrant set resulted in biases <0.4%. Using this method, we generated a high-resolution CCS database containing over 90 lipid values with HRIM. To test the applicability of this method to a broader class range typical of lipidomics experiments, a standard lipid mix was analyzed. The results highlight the importance of both class and arrival time range when correcting or scaling CCS values and provide guidance for implementation of the method for more general applications.

Tandem Trapped Ion Mobility Spectrometry/Mass Spectrometry (tTIMS/MS) Reveals Sequence-Specific Determinants of Top-Down Protein Fragment Ion Cross Sections

Top-down proteomics provides a straightforward approach to the level of proteoforms but remains technologically challenging. Using ion mobility spectrometry/mass spectrometry (IMS/MS) to separate top-down fragment ions improves signal/noise and dynamic range. Such applications, however, do not yet leverage the primary information obtained from IMS/MS, which is the characterization of the fragment ion structure by the measured momentum transfer cross sections. Here, we perform top-down analysis of intact proteins and assemblies using our tandem trapped ion mobility spectrometer/mass spectrometer (tTIMS/MS) and compile over 1400 cross section values of fragment ions. Our analysis reveals that most fragment ions exhibit multiple, stable conformations similar to those of intact polypeptides and proteins. The data further indicate that the conformational heterogeneity is strongly influenced by the amino acid sequences of the fragment ions. Moreover, time-resolved tTIMS/MS experiments reveal that conformations of top-down fragment ions can be metastable on the timescale of ion mobility measurements. Taken together, our analysis indicates that top-down fragment ions undergo a folding process in the gas phase and that this folding process can lead to kinetic trapping of intermediate states in ion mobility measurements. Hence, because the folding free energy surface of a polypeptide ion is encoded by its amino acid sequence and charge state, our analysis suggests that cross sections can be exploited as sequence-specific determinants of top-down fragment ions.

Recent developments in data acquisition, treatment and analysis with ion mobility-mass spectrometry for lipidomics

Lipids are involved in many biological processes and their study is constantly increasing. To identify a lipid among thousand requires of reliable methods and techniques. Ion Mobility (IM) can be coupled with Mass Spectrometry (MS) to increase analytical selectivity in lipid analysis of lipids. IM-MS has experienced an enormous development in several aspects, including instrumentation, sensitivity, amount of information collected and lipid identification capabilities. This review summarizes the latest developments in IM-MS analyses for lipidomics and focusses on the current acquisition modes in IM-MS, the approaches for the pre-treatment of the acquired data and the subsequent data analysis. Methods and tools for the calculation of Collision Cross Section (CCS) values of analytes are also reviewed. CCS values are commonly studied to support the identification of lipids, providing a quasi-orthogonal property that increases the confidence level in the annotation of compounds and can be matched in CCS databases. The information contained in this review might be of help to new users of IM-MS to decide the adequate instrumentation and software to perform IM-MS experiments for lipid analyses, but also for other experienced researchers that can reconsider their routines and protocols. This article is protected by copyright. All rights reserved.

Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein

Mass spectrometry and single molecule force microscopy are two experimental approaches able to provide structural information on intrinsically disordered proteins (IDPs). These techniques allow the dissection of conformational ensembles in their main components, although at a low-resolution level. In this work, we interpret the results emerging from these experimental approaches on human alpha synuclein (AS) by analyzing a previously published 73 μs-long molecular-dynamics (MD) simulation of the protein in explicit solvent. We further compare MD-based predictions of single molecule Förster resonance energy transfer (smFRET) data of AS in solution with experimental data. The combined theoretical and experimental data provide a description of AS main conformational ensemble, shedding light into its intramolecular interactions and overall structural compactness. This analysis could be easily transferred to other IDPs.

Cyclic Peptide Protomer Detection in the Gas Phase: Impact on CCS Measurement and Fragmentation Patterns

With the recent improvements in ion mobility resolution, it is now possible to separate small protomeric tautomers, called protomers. In larger molecules above 1000 Da such as peptides, a few studies suggest that protomers do exist as well and may contribute to their gas-phase conformational heterogeneity. In this work, we observed a CCS distribution that can be explained by the presence of protomers of surfactin, a small lipopeptide with no basic site. Following preliminary density functional theoretical calculations, several protonation sites in the gas phase were energetically favorable in positive ionization mode. Experimentally, at least three near-resolved IM peaks were observed in positive ionization mode, while only one was detected in negative ionization mode. These results were in good agreement with the DFT predictions. CID breakdown curve analysis after IM separation showed different inflection points (CE₅₀) suggesting that different intramolecular interactions were implied in the stabilization of the structures of surfactin. The fragment ratio observed after collision-induced fragmentation was also different, suggesting different ring-opening localizations. All these observations support the presence of protomers on the cyclic peptide moieties of the surfactin. These data strongly suggest that protomeric tautomerism can still be observed on molecules above 1000 Da if the IM resolving power is sufficient. It also supports that the proton localization involves a change in the 3D structure that can affect the experimental CCS and the fragmentation channels of such peptides.

Approaches to Heterogeneity in Native Mass Spectrometry

Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.

“Targeted Glucocorticoid Analysis using Ion Mobility-Mass Spectrometry (IM-MS)”

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Liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) for glucocorticoids.

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Determination of collision cross sections (CCS) for isomers.

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Different cation adducts shifted mobility and improved IM separation.

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Changing drift gas (He, Ar, CO₂) shifted mobility and improved resolution.

Introduction

Ion mobility-mass spectrometry (IM-MS) is an emerging technique in the -omics fields that has broad potential applicability to the clinical lab. As a rapid, gas-phase structure-based separation technique, IM-MS offers promise in isomer separations and can be easily combined with existing LC-MS methods (i.e., LC-IM-MS). Several experimental conditions, including analyte cation adducts and drift composition further provide a means to tune separations for global and/or targeted applications.

Objectives

The primary objective of this study was to demonstrate the utility of IM-MS under a range of experimental conditions for detection of glucocorticoids, and specifically for the separation of several isomeric pairs.

Methods

LC-IM-MS was used to characterize 16 glucocorticoids including three isomer pairs: cortisone/prednisolone, betamethasone/dexamethasone, and flunisolide/triamcinolone acetonide. Collision cross section (CCS) values were measured for all common adducts (e.g., protonated and sodiated) using both step-field and single-field methods. Alternative alkali, alkaline earth, and transition metals were introduced, such that their adducts could also be measured. Finally, four different drift gases (helium, nitrogen, argon, and carbon dioxide) were compared for their relative separation capability.

Results

LC-IM-MS offered a robust, multidimensional separation technique that allowed for the 16 glucocorticoids to be analyzed and separated in three-dimensions (retention time, CCS, and m/z). Despite the relatively modest resolution of isomer pairs under standard conditions (i.e., nitrogen drift gas, sodiated ions, etc.), improvements were observed for alkaline earth and transition metals (notable barium adducts) and in carbon dioxide drift gas.

Conclusion

In summary, LC-IM-MS offers potential as a clinical method due to its ease of coupling with traditional LC-MS methods and its promise for tuning separations to better resolve targeted and/or global isomers in complex biological samples.

Ultra-fast screening of free fatty acids in human plasma using ion mobility mass spectrometry

Free fatty acids involved in many metabolic regulations in human body. In this work, an ultra-fast screening method was developed for the analysis of free fatty acids using trapped ion mobility spectrometry coupled with mass spectrometry. Thirty-three free fatty acids possessing different unsaturation degrees and different carbon chain lengths were baseline separated and characterized within milliseconds. Saturated, monounsaturated, and polyunsaturated free fatty acids showed different linearities between collision cross section values and m/z. Establishment of correlations between structures and collision cross section values provided additional qualitative information and made it possible to determine free fatty acids which were out of the standards pool but possessed the confirmed linearity. Gas-phase separation made the quantitative analysis reliable and repeatable at a much lower time cost than chromatographic methods. The sensitivity was comparable to and even better than the reported results. The method was validated and applied to profiling free fatty acids in human plasma. Saturated free fatty acids abundance in the fasting state was found to be lower than that in the postprandial state, while unsaturated species abundance was found higher. The method was fast and robust with minimum sample pretreatment, so it was promising in high-throughput screening of free fatty acids. This article is protected by copyright. All rights reserved.

Toward Routine Analysis of Anabolic Androgenic Steroids in Urine Using Ion Mobility-Mass Spectrometry

Anabolic androgenic steroids (AAS) make up one of the most prevalent classes of performance-enhancing drugs banned by the World Anti-Doping Agency (WADA) due to the competitive advantage they can afford athletes. Mass spectrometry-based methods coupled with chromatographic separations have become the gold standard for AAS analysis because of the superior sensitivity and selectivity provided. However, emerging analytical techniques including ion mobility spectrometry (IMS) have been demonstrated in recent applications as a means to further characterize and identify potential unknowns while simultaneously delivering improved sensitivity by filtering noise. Herein we outline the next crucial steps in bringing IMS to the routine drug testing workflow by combining it with established chromatographic and mass spectrometry methods (i.e., LC-IM-MS) for the detection of AAS in human urine. In addition to robust measurement of collision cross sections which can be used for identification purposes, functional group microtrends provide a structural basis on which to elucidate the structure of future novel anabolic agents. Lastly, the developed workflow is tested by analysis of testosterone in a realistic matrix (human urine) and demonstrates a limit of detection of 524 pg/mL, which surpasses the WADA Minimum Required Performance Levels for anabolic steroids. This work is expected to pave the way toward routine incorporation of IMS into analytical drug testing workflows to augment both qualitative and quantitative measure of performance enhancing drugs in the future.

Insights and prospects for ion mobility-mass spectrometry in clinical chemistry

INTRODUCTION

Ion mobility-mass spectrometry is an emerging technology in the clinical setting for high throughput and high confidence molecular characterization from complex biological samples. Ion mobility spectrometry can provide isomer separations on the basis of molecular structure, the ability of which is increasing through technological developments that afford enhanced resolving power. Integrating multiple separation dimensions, such as liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) provide dramatic enhancements in the mitigation of molecular interferences for high accuracy clinical measurements.

AREAS COVERED

Multidimensional separations with LC-IM-MS provide better selectivity and sensitivity in molecular analysis. Mass spectrometry imaging of tissues to inform spatial molecular distribution is improved by complementary ion mobility analyses. Biomarker identification in surgical environments is enhanced by intraoperative biochemical analysis with mass spectrometry and holds promise for integration with ion mobility spectrometry. New prospects in high resolving power ion mobility are enhancing analysis capabilities, such as distinguishing isomeric compounds.

EXPERT OPINION

Ion mobility-mass spectrometry holds many prospects for the field of isomer identification, molecular imaging, and intraoperative tumor margin delineation in clinical settings. These advantages are afforded while maintaining fast analysis times and subsequently high throughput. High resolving power ion mobility will enhance these advantages further, in particular for analyses requiring high confidence isobaric selectivity and detection.

Trapped Ion Mobility Incorporated in LC-HRMS Workflows as an Integral Analytical Platform of High Sensitivity: Targeted and Untargeted 4D-Metabolomics in Extra Virgin Olive Oil

Trapped ion mobility spectrometry (TIMS) is a promising technique for the separation of isomers based on their mobility. In the present work, TIMS coupled to liquid chromatography (LC) and high-resolution mass spectrometry (HRMS) was applied as a comprehensive analytical platform to address authenticity challenges, focusing on extra virgin olive oil (EVOO). Isomers detected in EVOO's phenolic fraction, classified into secoiridoids group, were successfully separated. Thanks to parallel accumulation serial fragmentation (PASEF) acquisition mode, high-quality spectra were obtained, facilitating identification. Moreover, a four-dimensional (4D) untargeted metabolomics approach was implemented to evaluate EVOO's global profile in cases of both variety and geographical origin discrimination. Potential authenticity markers, attributed to isomers, were successfully identified through the proposed workflow that incorporates ion mobility information along with LC-HRMS analytical evidence (i.e., mass accuracy, retention time, isotopic pattern, MS/MS fragmentation). Our study establishes LC-TIMS-HRMS in food authenticity and highlights mobility-enhanced metabolomics in four dimensions.

A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry

Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.

Ultra-high pressure liquid chromatography coupled to travelling wave ion mobility-time of flight mass spectrometry for the screening of pharmaceutical metabolites in wastewater samples: Application to antiretrovirals

The presence of pharmaceutical compounds in the aquatic environment is a significant environmental health concern, which is exacerbated by recent evidence of the contribution of drug metabolites to the overall pharmaceutical load. In light of a recent report of the occurrence of metabolites of antiretroviral drugs (ARVDs) in wastewater, we investigate in the present work the occurrence of further ARVD metabolites in samples obtained from a domestic wastewater treatment plant in the Western Cape, South Africa. Pharmacokinetic data indicate that ARVDs are biotransformed into several positional isomeric metabolites, only two of which have been reported wastewater samples. Given the challenges associated with the separation and identification of isomeric species in complex wastewater samples, a method based on liquid chromatography hyphenated to ion mobility spectrometry-high resolution mass spectrometry (LC-IMS-HR-MS) was implemented. Gradient LC separation was achieved on a sub-2 µm reversed phase column, while the quadrupole-time-of-flight MS was operated in data independent acquisition (DIA) mode to increase spectral coverage of detected features. A mass defect filter (MDF) template was implemented to detect ARVD metabolites with known phase I and phase II mass shifts and fractional mass differences and to filter out potential interferents. IMS proved particularly useful in filtering the MS data for co-eluting species according to arrival time to provide cleaner mass spectra. This approach allowed us to confirm the presence of two known hydroxylated efavirenz and nevirapine metabolites using authentic standards, and to tentatively identify a carboxylate metabolite of abacavir previously reported in literature. Furthermore, three hydroxylated-, two sulphated and one glucuronidated metabolite of efavirenz, two hydroxylated metabolites of nevirapine and one hydroxylated metabolite of ritonavir were tentatively or putatively identified in wastewater samples for the first time. Assignment of the metabolites is discussed in terms of high resolution fragmentation data, while collisional cross section (CCS) values measured for the detected analytes are reported to facilitate further work in this area.

Plants Metabolome Study: Emerging Tools and Techniques

Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

Integration of Mass Spectrometry Data for Structural Biology

Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.

Implications of Blanc's Law for Use in Trapped Ion Mobility Spectrometry

Blanc's Law has served as a way to predict the mobilities of ions in mixed drift gases for over 100 years yet has remained largely unexplored using newer ion mobility spectrometry (IMS) configurations, including traveling wave and trapped IMS (TIMS) systems. Here, we evaluate a drift-tube IMS (DTIMS) and compare it to a similar set of experiments performed in TIMS. We found that Blanc's Law can be applied in a DTIMS to determine the mobility of an analyte in the minor gas component of a ternary mixed drift gas system within 2% error. Additionally, the calibration procedure for TIMS to convert elution voltages into a mobility value corrects for significant deviations (>4%) from Blanc's Law in the elution voltage domain. For the range of gas identities probed in this effort, up to an 11% error in calibrated mobilities was observed when using a gas mixture in the TIMS that differed from the gas used for the reference mobility. However, when the gas mixture within the TIMS was the same as the respective calibrant mobilities, calibration errors within the TIMS were as low as 0.01%. Interestingly, when probing the behavior of ions with argon-containing mixtures within the TIMS, the current accepted paradigm of elution voltage being proportional to inverse mobilities in TIMS calibrations procedures was shown to deviate substantially from the trends observed with DTIMS measurements. With this initial effort, foundations for future mixed drift gas measurements in TIMS are set for expanded analyte classes and larger molecules.

Predicting differential ion mobility behaviour in silico using machine learning

Although there has been a surge in popularity of differential mobility spectrometry (DMS) within analytical workflows, determining separation conditions within the DMS parameter space still requires manual optimization. A means of accurately predicting differential ion mobility would benefit practitioners by significantly reducing the time associated with method development. Here, we report a machine learning (ML) approach that predicts dispersion curves in an N2 environment, which are the compensation voltages (CVs) required for optimal ion transmission across a range of separation voltages (SVs) between 1500 to 4000 V. After training a random-forest based model using the DMS information of 409 cationic analytes, dispersion curves were reproduced with a mean absolute error (MAE) of ≤ 2.4 V, approaching typical experimental peak FWHMs of ±1.5 V. The predictive ML model was trained using only m/z and ion-neutral collision cross section (CCS) as inputs, both of which can be obtained from experimental databases before being extensively validated. By updating the model via inclusion of two CV datapoints at lower SVs (1500 V and 2000 V) accuracy was further improved to MAE ≤ 1.2 V. This improvement stems from the ability of the "guided" ML routine to accurately capture Type A and B behaviour, which was exhibited by only 2% and 17% of ions, respectively, within the dataset. Dispersion curve predictions of the database's most common Type C ions (81%) using the unguided and guided approaches exhibited average errors of 0.6 V and 0.1 V, respectively.

Biocompatible MXene (Ti3C2Tx) Immobilized with Flavin Adenine Dinucleotide as an Electrochemical Transducer for Hydrogen Peroxide Detection in Ovarian Cancer Cell Lines

Flavin adenine dinucleotide (FAD) is a coenzyme and acts as a redox cofactor in metabolic process. Owing to such problems as poor electron transfer properties, unfavorable adsorption, and lack of stability on rigid electrodes, the bio-electrochemical applications of FAD have been limited. Herein, a novel fabrication method was developed for the immobilization process using 2D MXene (Ti₃C₂T_x), which enhanced the redox property of FAD and improved the electro-catalytic reduction of hydrogen peroxide (H₂O₂) in neutral medium. The FAD-immobilized Ti₃C₂T_x electrode (FAD/Ti₃C₂T_x) was studied by UV-Visible and Raman spectroscopies, which confirmed the successful adsorption of FAD on the Ti₃C₂T_x surface. The surface morphology and the elemental composition of Ti₃C₂T_x were investigated by high resolution transmission electron microscopy and the energy dispersive X-ray analysis. The redox property of the FAD/Ti₃C₂T_x modified glassy carbon electrode (FAD/Ti₃C₂T_x/GCE) was highly dependent on pH and exhibited a stable redox peak at −0.455 V in neutral medium. Higher amounts of FAD molecules were loaded onto the 2D MXene (Ti₃C₂T_x)-modified electrode, which was two times higher than the values in the reported work, and the surface coverage (ᴦ_FAD) was 0.8 × 10⁻¹⁰ mol/cm². The FAD/Ti₃C₂T_x modified sensor showed the electrocatalytic reduction of H₂O₂ at −0.47 V, which was 130 mV lower than the bare electrode. The FAD/Ti₃C₂T_x/GCE sensor showed a linear detection of H₂O₂ from 5 nM to 2 µM. The optimization of FAD deposition, amount of Ti₃C₂T_x loading, effect of pH and the interference study with common biochemicals such as glucose, lactose, dopamine (DA), potassium chloride (KCl), ascorbic acid (AA), amino acids, uric acid (UA), oxalic acid (OA), sodium chloride (NaCl) and acetaminophen (PA) have been carried out. The FAD/Ti₃C₂T_x/GCE showed high selectivity and reproducibility. Finally, the FAD/Ti₃C₂T_x modified electrode was successfully applied to detect H₂O₂ in ovarian cancer cell lines.

Modular Ion Mobility Calibrants for Organometallic Anions Based on Tetraorganylborate Salts

Organometallics are widely used in catalysis and synthesis. Their analysis relies heavily on mass spectrometric methods, among which traveling-wave ion mobility spectrometry (TWIMS) has gained increasing importance. Collision cross sections (CCS) obtainable by TWIMS significantly aid the structural characterization of ions in the gas phase, but for organometallics, their accuracy has been limited by the lack of appropriate calibrants. Here, we propose tetraorganylborates and their alkali-metal bound oligomers [M_n-1(BR₄)_n]^- (M = Li, Na, K, Rb, Cs; R = aryl, Et; n = 1-6) as calibrants for electrospray ionization (ESI) TWIMS. These species chemically resemble typical organometallics and readily form upon negative-ion mode ESI of solutions of alkali-metal tetraorganylborates. By combining different tetraorganylborate salts, we have generated a large number of anions in a modular manner and determined their CCS values by drift-tube ion mobility spectrometry (DTIMS) (^DTCCS_He = 81-585, ^DTCCS_N2 = 130-704 Ų). In proof-of-concept experiments, we then applied these ^DTCCS values to the calibration of a TWIMS instrument and analyzed phenylcuprate and argentate anions, [Li_n-1M_nPh_2n]^- and [M_nPh_n+1]^- (M = Cu, Ag), as prototypical reactive organometallics. The ^TWCCS_N2 values derived from TWIMS measurements are in excellent agreement with those determined by DTIMS (<2% relative difference), demonstrating the effectiveness of the proposed calibration scheme. Moreover, we used theoretical methods to predict the structures and CCS values of the anions considered. These predictions are in good agreement with the experimental results and give further insight into the trends governing the assembly of tetraorganylborate, cuprate, and argentate oligomers.

Rapid characterization and pharmacokinetic study of aristolochic acid analogues using ion mobility mass spectrometry

Aristolochic acid analogues (AAAs), naturally existing in herbal Aristolochia and Asarum genera, were once widely used in traditional pharmacopeias because of their anti-inflammatory properties, but lately they were identified as potential nephrotoxins and mutagens. A method for rapid characterization of AAAs in serum was developed using ion mobility spectrometry coupled with mass spectrometry (IMS-MS). Five AAAs, containing four aristolochic acids and one aristolactam, were separated and identified within milliseconds. AAAs were separated in gas phase based on the difference of their ion mobility (K0), and then identified based on their K0 values, m/z, and product ions from MS/MS. Quantitative analysis of AAAs was performed using an internal standard with a satisfactory sensitivity. Limits of detection (signal-to-noise = 3) and quantification (signal-to-noise = 10) were 1-5 ng/mL and 3-8 ng/mL, respectively. The method was validated and successfully applied to the pharmacokinetics study of AAAs in rats, offering a promising way for fast screening and evaluation of AAAs in biological samples.

Determining Collision Cross Sections from Differential Ion Mobility Spectrometry

The experimental determination of ion-neutral collision cross sections (CCSs) is generally confined to ion mobility spectrometry (IMS) technologies that operate under the so-called low-field limit or those that enable empirical calibration strategies (e.g., traveling wave IMS; TWIMS). Correlation of ion trajectories to CCS in other non-linear IMS techniques that employ dynamic electric fields, such as differential mobility spectrometry (DMS), has remained a challenge since its inception. Here, we describe how an ion's CCS can be measured from DMS experiments using a machine learning (ML)-based calibration. The differential mobility of 409 molecular cations (m/z: 86-683 Da and CCS 110-236 Å2) was measured in a N2 environment to train the ML framework. Several open-source ML routines were tested and trained using DMS-MS data in the form of the parent ion's m/z and the compensation voltage required for elution at specific separation voltages between 1500 and 4000 V. The best performing ML model, random forest regression, predicted CCSs with a mean absolute percent error of 2.6 ± 0.4% for analytes excluded from the training set (i.e., out-of-the-bag external validation). This accuracy approaches the inherent statistical error of ∼2.2% for the MobCal-MPI CCS calculations employed for training purposes and the <2% threshold for matching literature CCSs with those obtained on a TWIMS platform.

Identification of N-glycan oligomannoside isomers in the diatom Phaeodactylum tricornutum

Microalgae are emerging production systems for recombinant proteins like monoclonal antibodies. In this context, the characterization of the host cell N-glycosylation machinery and of the microalgae-made biopharmaceuticals, which are mainly glycoprotein-based products, requires efficient analytical methodologies dedicated to the profiling of the N-glycans. Herein, in order to gain knowledge regarding its N-glycosylation pathway, we profile the protein N-linked oligosaccharides isolated from the diatom Phaeodactylum tricornutum that has been used successfully to produce functional monoclonal antibodies. The combination of ion mobility spectrometry-mass Spectrometry and electrospray ionization-multistage tandem mass spectrometry allows us to decipher the detailed structure of the oligomannoside isomers and to demonstrate that the processing of the oligomannosides N-linked to proteins occurs in this diatom as reported in mammals. Therefore, P. tricornutum synthesizes human-like oligomannosides in contrast to other microalgae species. This represent an advantage as an alternative ecofriendly expression system to produce biopharmaceuticals used for human therapy.

Comprehensive Composition, Structure, and Size Characterization for Thiophene Compounds in Petroleum Using Ultrahigh-Resolution Mass Spectrometry and Trapped Ion Mobility Spectrometry

Thiophene compounds are the main concern of petroleum desulfurization, and their chemical composition and molecular configuration have critical impacts on thermodynamic and kinetic processes. In this work, atmospheric pressure chemical ionization (APCI) was employed for effective ionization of thiophene compounds in petroleum with complex matrix, in which carbon disulfide was used for generating predominant [M]^+• ions without the need of derivatization as for electrospray ionization. APCI coupled with ultrahigh-resolution mass spectrometry (UHRMS) was successfully applied to the composition characterization of thiophene compounds in both a low boiling petroleum fraction and a whole crude oil. APCI coupled with trapped ion mobility spectrometry (TIMS) was developed to determine the shape and size of thiophene compounds, providing configuration information that affects the steric hindrance and diffusion behavior of reactants in the desulfurization reaction, which has not been previously reported. Moreover, the comprehensive experimental structural data, expressed as the collision cross section (CCS) of the ions as surrogates of molecules, provided clues to the factors affecting the desulfurization reactivity of thiophene compounds. Further exploration showed that not only qualitative analysis of thiophene compounds can be achieved from the correlation between m/z and CCS, but also molecular size was found to be correlated with CCS that can be used as structural analysis. Overall, the molecular composition and dimension analysis together can provide substantial information for the desulfurization activity of thiophene compounds, facilitating the desulfurization process studies and catalyst design.