Exploring the potential of high-resolution LC-MS in combination with ion mobility separation and surrogate minimal depth for enhanced almond origin authentication

Almonds (Prunus dulcisMill.) are consumed worldwide and their geographical origin plays a crucial role in determining their market value. In the present study, a total of 250 almond reference samples from six countries (Australia, Spain, Iran, Italy, Morocco, and the USA) were non-polar extracted and analyzed by UPLC-ESI-IM-qToF-MS. Four harvest periods, more than 30 different varieties, including both sweet and bitter almonds, were considered in the method development. Principal component analysis showed that there are three groups of samples with similarities: Australia/USA, Spain/Italy and Iran/Morocco. For origin determination, a random forest achieved an accuracy of 88.8 %. Misclassifications occurred mainly between almonds from the USA and Australia, due to similar varieties and similar external influences such as climate conditions. Metabolites relevant for classification were selected using Surrogate Minimal Depth, with triacylglycerides containing oxidized, odd chained or short chained fatty acids and some phospholipids proven to be the most suitable marker substances. Our results show that focusing on the identified lipids (e. g., using a QqQ-MS instrument) is a promising approach to transfer the origin determination of almonds to routine analysis.

Serum untargeted lipidomic characterization in a general Chinese cohort with residual per-/polyfluoroalkyl substances by liquid chromatography-drift tube ion mobility-mass spectrometry

Per- and polyfluoroalkyl substances (PFAS) remain controversial due to their high persistency and potential human toxicity. Although occupational exposure to PFAS has been widely investigated, the implications of PFAS occurrence in the general population remain to be unraveled. Considering that serum from most people contains PFAS, the aim of this study was to characterize the lipidomic profile in human serum from a general cohort (n = 40) with residual PFAS levels. The geometric means of ∑PFAS (11.8 and 4.4 ng/mL) showed significant differences (p < 0.05) for the samples with the highest (n = 20) and lowest (n = 20) concentrations from the general population respectively. Reverse-phase liquid chromatography coupled to drift tube ion mobility and high-resolution mass spectrometry using dual polarity ionization was used to characterize the lipid profile in both groups. The structural elucidation involved the integration of various parameters, such as retention time, mass-to-charge ratio, tandem mass spectra and collision cross section values. This approach yielded a total of 20 potential biomarkers linked to the perturbed glycerophospholipid metabolism, energy metabolism and sphingolipid metabolism. Among these alterations, most lipids were down-regulated and some specific lipids (PC 36:5, PC 37:4 and PI O-34:2) exhibited a relatively strong Spearman correlation and predictive capacity for PFAS contamination. This study could support further toxicological assessments and mechanistic investigations into the effects of PFAS exposure on the lipidome.

Using differential mobility spectrometry to improve the specificity of targeted measurements of 2,3-dinor 11β-Prostaglandin F2α

INTRODUCTION

2,3-dinor 11β-Prostaglandin F2α (BPG) is an arachidonic acid derivative and the most abundant metabolic byproduct of prostaglandin D2, which is released during mast cell activation. Therefore, measurements of BPG in urine using liquid chromatography-tandem mass spectrometry (LC-MS/MS) provide a noninvasive method for evaluation and management of mast cell disorders. Measurements obtained by LC-MS/MS exhibit a high prevalence of chromatographic interferences resulting in challenges with optimal determination of BGP. In this investigation, differential mobility spectrometry (DMS) is utilized to overcome the limitations of current testing.

METHODS

Urine samples were extracted using an automated solid-phase extraction method. Samples were then analyzed with and without DMS devices installed on two commercially available mass spectrometry platforms to assess the benefits of DMS. Following promising results from a preliminary analytical evaluation, LC-DMS-MS/MS measurements of BPG in urine were fully validated to assess the analytical implications of using this technology.

RESULTS AND DISCUSSION

The addition of DMS devices to the LC-MS/MS systems evaluated in this investigation significantly reduced interferences observed in the chromatograms. Concomitantly, DMS reduced the number of discordant quantifier/qualifier fragment ion results that significantly exceeded the ± 20 % limits, suggesting greater analytical specificity. The validation studies yielded low interday imprecision, with %CVs less than 6.5 % across 20 replicate measurements. Validation studies assessing other aspects of analytical performance also met acceptance criteria.

CONCLUSIONS

Incorporating DMS devices greatly improved the specificity of BPG measurements by LC-MS/MS, as evidenced by the comparison of chromatograms and fragment ion results. Validation studies showed exceptional performance for established analytical metrics, indicating that this technology can be used to minimize the impact of interferences without adversely impacting other aspects of analytical or clinical performance.

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling

The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation. Furthermore, charge localization was seen to be correlated with CCS prediction accuracy and with gas-phase proton affinity demonstrating the potential to provide a proxy for prediction error based on chemical structural properties. The presented approach and findings represent a further step towards accurate prediction and application of computationally generated CCS values.

CE-MS/MS and CE-timsTOF to separate and characterize intramolecular disulfide bridges of monoclonal antibody subunits and their application for the assessment of subunit reduction protocols

Characterization at the subunit level enables detailed mass spectrometric characterization of posttranslational modifications (PTMs) of monoclonal antibodies (mAbs). The implemented reduction often leaves the intramolecular disulfide bridges intact. Here, we present a capillary electrophoretic (CE) method based on a neutral-coated capillary for the separation of immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) digested and reduced mAb subunits followed by mass spectrometry (MS), MS/MS identification, and trapped ion mobility mass spectrometry (timsTOF). Our CE approach enables the separation of (i) different subunit moieties, (ii) various reduction states, and (iii) positional isomers of these partly reduced subunit moieties. The location of the remaining disulfide bridges can be determined by middle-down electron transfer higher energy collisional dissociation (EThcD) experiments. All these CE-separated variants show differences in ion mobility in the timsTOF measurements. Applying the presented CE-MS/MS method, reduction parameters such as the use of chaotropic salts were studied. For the investigated antibodies, urea improved the subunit reduction significantly, whereas guanidine hydrochloride (GuHCl) leads to multiple signals of the same subunit in the CE separation. The presented CE-MS method is a powerful tool for the disulfide-variant characterization of mAbs on the subunit level. It enables understanding disulfide bridge reduction processes in antibodies and potentially other proteins.

Increasing coverage of the urinary polar metabolome using ultra high-performance hydrophobic interaction liquid chromatography combined with linear and cyclic travelling wave ion mobility and mass spectrometry

The use of HILIC-based separations for the analysis of polar metabolites in metabolic phenotyping studies is well established. Here, we demonstrate the increased coverage of the polar metabolome obtained by travelling wave (TW) ion mobility (IM) instruments combined with HILIC and mass spectrometry (MS) for metabotyping rat and mouse urine samples. Profiling was performed using either a linear TW IM-MS based instrument with a path length of 40 cm or an instrument with a cyclic travelling wave analyser (cIM) with a path length of 95 cm. Due to the added resolution afforded by using both the linear and cyclic IM geometries with MS detection (IM-MS) significant increases in feature count (m/z-tR pairs) were generally obtained compared to HILIC-MS alone. In addition, the use of both linear and cyclic IM-MS improved the quality of the mass spectra obtained as a result of the separation of co-eluting analytes. As would be expected from the increased path length of the cyclic IM-MS instrument compared to the linear device, the largest gains in feature detection were obtained for the HILIC-cIM-MS combination. By increasing the resolution of coeluting components, the cyclic IM-MS instrumentation also provided the largest improvement in the quality of the mass spectral data obtained. When applied to mouse urines obtained from both control and gefitinib-dosed mice, time-related changes were detected in those obtained from the treated animals that were not seen in the controls. Polar metabolites affected by drug administration included, but were not limited to, hypoxanthine, 1,3-dimethyluracil and acetylcarnitine. The changes seen in the relative concentrations of these endogenous metabolites appeared to be related to drug concentrations in the plasma and urine suggesting a pharmacometabodynamic link.

The analysis of the migration of per and poly fluoroalkyl substances (PFAS) from food contact materials using ultrahigh performance liquid chromatography coupled to ion-mobility quadrupole time-of-flight mass spectrometry (UPLC- IMS-QTOF)

Per-poly fluoroalkyl substances (PFASs) are a group of synthetic fluorine compounds used in food packaging materials to repel water and fats. This study assessed the chemical migration of PFAS from different food contact materials, including cardboard, recycled cardboard, biopolymer, paper and Teflon trays, from various markets. Migration assays were conducted using Tenax® as a food simulant, which was optimized by subjecting it to three consecutive extractions with 3 mL of ethanol within an hour. The resulting extractions were combined and concentrated to 0.5 mL using a nitrogen stream. The analysis was performed using ultrahigh performance liquid chromatography (UPLC) coupled with ion-mobility (IMS) quadrupole-time-of-flight (QTOF) mass spectrometry, which provided a powerful and novel tool for identifying a library of targets containing collision cross section values (CCS) and increasing confidence in subsequent identifications. Eleven PFAS compounds belonging to the family of perfluorocarboxylic acid, perfluorosulfonic acid and perfluorooctanesulfonamidoacetic acid substances (PFCAs, PFSAs and FOSAAs) were found in packaging samples obtained from China, with migrant concentrations ranging 3.2 and 22.3 μg/kg. In contrast, no detectable levels of PFAS were observed in packaging samples obtained in Spain. All trays tested were deemed to be suitable for use as food contact materials due to the fact that their migrant values were lower than 0.025 mg/kg for PFOA and its salts, and lower than a maximum concentration of 1 mg/kg for PFOA-related compounds.

In situ separation and visualization of isomeric auxin derivatives in Arabidopsis by ion mobility mass spectrometry imaging

In situ separation and visualization of synthetic and naturally occurring isomers from heterogeneous plant tissues, especially when they share similar molecular structures, are a challenging task. In this study, we combined the ion mobility separation with desorption electrospray ionization mass spectrometry imaging (DESI-IM-MSI) to achieve a direct separation and visualization of two synthetic auxin derivatives, auxinole and its structural isomer 4pTb-MeIAA, as well as endogenous auxins from Arabidopsis samples. Distinct distribution of these synthetic isomers and endogenous auxins in Arabidopsis primary roots and hypocotyls was achieved in the same imaging analysis from both individually treated and cotreated samples. We also observed putative metabolites of synthetic auxin derivatives, i.e. auxinole amino acid conjugates and hydrolysed 4pTb-MeIAA product - 4pTb-IAA, based on their unique drifting ion intensity patterns. Furthermore, DESI-IM-MSI-revealed abundance of endogenous auxins and synthetic isomers was validated by liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that DESI-IM-MSI could be used as a robust technique for detecting endogenous and exogenous isomers and provide a spatiotemporal evaluation of hormonomics profiles in plants.

Autocatalysis in Eschenmoser Coupling Reactions

The Eschenmoser coupling reaction (ECR) of thioamides with electrophiles is believed to proceed via thiirane intermediates. However, little is known about converting the intermediates into ECR products. Previous mechanistic studies involved external thiophiles to remove the sulfur atom from the intermediates. In this work, an ECR proceeding without any thiophilic agent or base is studied by electrospray ionization-mass spectrometry. ESI-MS enables the detection of the so-far elusive polysulfide species Sn , with n ranging from 2 to 16 sulfur atoms, proposed to be the key species leading to product formation. Integrating observations from ion mobility spectrometry, ion spectroscopy, and reaction monitoring via flow chemistry coupled with mass spectrometry provides a comprehensive understanding of the reaction mechanism and uncovers the autocatalytic nature of the ECR reaction.

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.

Peptide collision cross sections of 22 post-translational modifications

Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.

Evaluating dynamic traveling wave profiles for the enhancement of separation and sensitivity in traveling wave structures for lossless ion manipulations

The amenability of traveling wave ion mobility spectrometry (TWIMS) to extended separation pathlengths has prompted a recent surge of interest concerning the technique. While promising, the optimization of ion transmission, particularly when analyzing increasingly disparate species, remains an obstacle in TWIMS. To address this issue, we evaluated a suite of dynamic TW profiles using an original TW structures for lossless ion manipulations (TW-SLIM) platform developed at Washington State University. Inspired by the range of gradient elution profiles used in traditional chromatography, three distinct square TW profiles were evaluated: a static approach which represents a traditional waveform, a dual approach which consists of two distinct TW profiles within a given separation event; and a ramp approach which varies TW speed and amplitude at a fixed rate during separation. The three waveform profiles were evaluated in terms of their impact on separation (quantified as resolution) and sensitivity (quantified using signal-to-noise ratio (SNR), and ion abundance). Concerning separation, the highest resolution (R) was observed when operating with the static waveform (R = 7.92); however, the ramp waveform performed comparably (R = 7.70) under similar conditions. Regarding SNR, optimum waveform profiles were species dependent. Bradykinin2+ displayed the largest gains in SNR (36.6% increase) when ramping TW speed, while the gains were greatest (33.5% increase) for tetraoctylammonium when modulating TW amplitude with the static waveform. Lastly, significant (>10%) increases in the abundance of tetraoctylammonium ions were observed exclusively when utilizing a ramped waveform. The present set of experiments outline the results and challenges related to optimizing separations using alternative TW profiles and provides insight concerning TW-SLIM method development which may be tailored to enhance select analytical metrics.

Trapped ion mobility mass spectrometry of new psychoactive substances: Isomer-specific identification of ring-substituted cathinones

New psychoactive substances (NPS) are synthetic derivatives of illicit drugs designed to mimic their psychoactive effects. NPS are typically not controlled under drug acts or their legal status depends on their molecular structure. Discriminating isomeric forms of NPS is therefore crucial for forensic laboratories. In this study, a trapped ion mobility spectrometry time-of-flight mass spectrometry (TIMS-TOFMS) approach was developed for the identification of ring-positional isomers of synthetic cathinones, a class of compounds representing two-third of all NPS seized in Europe in 2020. The optimized workflow features narrow ion-trapping regions, mobility calibration by internal reference, and a dedicated data-analysis tool, allowing for accurate relative ion-mobility assessment and high-confidence isomer identification. Ortho-, meta- and para-isomers of methylmethcathinone (MMC) and bicyclic ring isomers of methylone were assigned based on their specific ion mobilities within 5 min, including sample preparation and data analysis. The resolution of two distinct protomers per cathinone isomer added to the confidence in identification. The developed approach was successfully applied to the unambiguous assignment of MMC isomers in confiscated street samples. These findings demonstrate the potential of TIMS-TOFMS for forensic case work requiring fast and highly-confident assignment cathinone-drug isomers in confiscated samples.

Collision cross-section as a universal molecular descriptor in the analysis of PFAS and use of ion mobility spectrum filtering for improved analytical sensitivities

The massive usage of per- and polyfluoroalkyl substances (PFAS), as well as their high chemical stability, have led to their ubiquitous presence in environmental matrices and direct human exposure through contaminated food, particularly fish. In the analysis of this large group of substances, the use of ion mobility coupled to mass spectrometry is of particular relevance because it uses an additional descriptor, the collision cross-section (CCS), which results in increased selectivity. In the present work, the ^TWCCS_N2 of 24 priority PFAS were experimentally obtained, and the reproducibility of these measurements was evaluated over seven weeks. The average values were employed to critically assess previously reported data and theoretical calculations. This gain in selectivity made it possible to increase the sensitivity of the detection on complex matrices (biota, food and human serum) by using the drift time associated to each analyte as a filter, thus reducing the interferences and background noise and allowing their detection at trace levels.

Separation of flavonoid isomers by cyclic ion mobility mass spectrometry

Analytical techniques, such as liquid chromatography coupled to mass spectrometry (LC-MS) or nuclear magnetic resonance (NMR), are widely used for characterization of complex mixtures of (isomeric) proteins, carbohydrates, lipids, and phytochemicals in food. Food can contain isomers that are challenging to separate, but can possess different reactivity and bioactivity. Catechins are the main phenolic compounds in tea; they can be present as various stereoisomers, which differ in their chemical properties. Currently, there is a lack of fast and direct methods to monitor interconversion and individual reactivity of these epimers (e.g. epicatechin (EC) and catechin (C)). In this study, cyclic ion mobility mass spectrometry (cIMS-MS) was explored as a potential tool for the separation of catechin epimers. Formation of sodium and lithium adducts enhanced IMS separation of catechin epimers, compared to deprotonation and protonation. Baseline separation of the sodium adducts of catechin epimers was achieved. Moreover, we developed a fast method for the identification and semi-quantification of cIMS-MS separated catechin epimers. With this method, it is possible to semi-quantify the ratio between EC and C (1:5 to 5:1, within 50-1200 ng mL^-1) in food samples, such as tea. Finally, the newly developed approach for cIMS-MS separation of flavonoids was demonstrated to be successful in separation of two sets of positional isomers (i.e. morin, tricetin, and quercetin; and kaempferol, fisetin, luteolin, and scutellarein). To conclude, we showed that both epimers and positional isomers of flavonoids can be separated using cIMS-MS, and established the potential of this method for challenging flavonoid separations.

LC-IMS-HRMS for identification of biomarkers in untargeted metabolomics: The effects of pterostilbene and resveratrol consumption in liver steatosis, animal model

Untargeted metabolomics with the combination of ion mobility separation coupled to high resolution mass spectrometry (IMS-HRMS) was applied to investigate the impact of resveratrol and pterostilbene supplementation on the metabolic fingerprint of the Wistar rats liver with induced liver steatosis. RP-LC and HILIC in both ionisation modes were employed to analyse the liver samples (n = 40) from Wistar rats fed with a high-fat and high-fructose diet, supplemented or not with resveratrol and pterostilbene. After univariate and multivariate statistical analysis, 34 metabolites were highlighted in the different diets and elucidated. Despite the structural similarity, different alterations in liver metabolism were observed by the supplementations. Resveratrol treatment was characterised by the alteration in metabolism of 17 lysophospholipids, while pterostilbene affected some vitamins and derivatives, among others. IMS has demonstrated great potential in the elucidation process thanks to the additional structural descriptor the CCS (Ų), providing more confidence in the identification.

Untargeted metabolomics approach using UHPLC-IMS-QTOF MS for surface body samples to identify low-volatility chemosignals related to maternal care in mice

The present study is focused on the determination of low-volatile chemosignals excreted or secreted by mouse pups in their early days of life involved in maternal care induction in mice adult females. Untargeted metabolomics was employed to differentiate between samples collected with swabs from facial and anogenital area from neonatal mouse pups receiving maternal care (first two weeks of life) and the elder mouse pups in the weaning period (4th week old). The sample extracts were analysed by ultra-high pressure liquid chromatography (UHPLC) coupled to ion mobility separation (IMS) in combination with high resolution mass spectrometry (HRMS). After data processing with Progenesis QI and multivariate statistical analysis, five markers present in the first two weeks of mouse pups life and putatively involved in materno-filial chemical communication were tentatively identified: arginine, urocanic acid, erythro-sphingosine (d17:1), sphingosine (d18:1) and sphinganine. The four-dimensional data and the tools associated to the additional structural descriptor obtained by IMS separation were of great help in the compound identification. The results demonstrated the great potential of UHPLC-IMS-HRMS based untargeted metabolomics to identity putative pheromones in mammals.

Discovery of Food Intake Biomarkers Using Metabolomics

Due to the high impact of diet exposure on health, it is crucial the generation of robust data of regular dietary intake, hence improving the accuracy of dietary assessment. The metabolites derived from individual food or group of food have great potential to become biomarkers of food intake (BFIs) and provide more objective food consumption measurements.Herein, it is presented an untargeted metabolomic workflow for the discovery BFIs in blood and urine samples, from the study design to the biomarker identification. Samples are analyzed by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). A wide variety of compounds are covered by separate analyses of medium to nonpolar molecules and polar metabolites based on two LC separations as well as both positive and negative electrospray ionization. The main steps of data treatment of the comprehensive data sets and statistical analysis are described, as well as the principal considerations for the BFI identification.

Rapid identification of pyoverdines of fluorescent Pseudomonas spp. by UHPLC-IM-MS

Siderophores are iron-chelating molecules produced by bacteria and other microbes. They are involved with virulence in infections and play key roles in bacterial community assembly and as plant protectants due to their pathogen control properties. Although assays exist to screen whether newly isolated bacteria can produce siderophores, the chemical structures of many of these bio-active molecules remain unidentified due to the lack of rapid analytical procedures. An important group of siderophores are pyoverdines. They consist of a structurally diverse group of chromopeptides, whose amino acid sequence is characteristic for the fluorescent Pseudomonas species that secrets them. Although over 60 pyoverdine structures have been described so far, their characterization is cumbersome and several methods (isoelectrofocusing, iron uptake measurement, mass determination) are typically combined as ambiguous results are often achieved by a single method. Those additional experiments consume valuable time and resources and prevent high-throughput analysis. In this work, we present a new pyoverdine characterisation option by recording their collision cross sections (CCS) using trapped ion mobility spectrometry. This can be done simultaneously in combination with UHPLC and high-resolution MS resulting in a rapid identification of pyoverdines. The high specificity of CCS values is presented for 17 pyoverdines secreted by different Pseudomonas strains. The pyoverdine mass determination by full scan MS was supported by fragments obtained from broadband collision induced dissociation (bbCID). As iron contaminations in laboratories are not uncommon, CCS values of ferripyoverdines were also evaluated. Thereby, unusual and highly characteristic ion mobility patterns were obtained that are suitable as an alternative identification marker.

Guidelines and considerations for building multidimensional libraries for untargeted MS-based metabolomics

INTRODUCTION

Feature annotation is crucial in untargeted metabolomics but remains a major challenge. The large pool of metabolites collected under various instrumental conditions is underrepresented in publicly available databases. Retention time (RT) and collision cross section (CCS) measurements from liquid chromatography ion mobility high-resolution mass spectrometers can be employed in addition to MS/MS spectra to improve the confidence of metabolite annotation. Recent advancements in machine learning focus on improving the accuracy of predictions for CCS and RT values. Therefore, high-quality experimental data are crucial to be used either as training datasets or as a reference for high-confidence matching.

METHODS

This manuscript provides an easy-to-use workflow for the creation of an in-house metabolite library, offers an overview of alternative solutions, and discusses the challenges and advantages of using open-source software. A total of 100 metabolite standards from various classes were analyzed and subjected to the described workflow for library generation.

RESULTS AND DISCUSSION

The outcome was an open-access available NIST format metabolite library (.msp) with multidimensional information. The library was used to evaluate CCS prediction tools, MS/MS spectra heterogeneities (e.g., multiple adducts, in-source fragmentation, radical fragment ions using collision-induced dissociation), and the reporting of RT.

Characterization of lipid carbon-carbon double-bond isomerism via ion mobility-mass spectrometry (IMS-MS) combined with cuprous ion-induced fragmentation

Characterization of phospholipid isomers is challenging due to their identical masses and similarities in structures. Here, we report that copper (I) ion complexed with phospholipids can be used to characterize both carbon-carbon double-bond (C=C bond) positional and geometric isomers. We investigate the distinct fragmentation patterns induced by the π-Cu+ interaction and developed strategies to rapidly characterize the isomerism of phospholipids. The multi-stage fragmentation of Cu+-adducted lipids by collision-induced dissociation can generate diagnostic ions to locate C=C bonds in unsaturated lipids. Furthermore, the collision cross sections of Cu+-adducted parent lipids and product ions can be used as molecular descriptors in distinguishing C=C bond geometric isomers. A bovine heart lipid extract containing Z-configuration lipids spiked with an E-configuration lipid was analyzed to demonstrate rapidness and effectiveness of the method in distinguishing lipid geometric isomers from a real sample.

High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF

Ion mobility separation is becoming an integral part in mass spectrometry-based proteomics. Here we describe the use of a trapped ion mobility-quadrupole time-of-flight (TIMS-QTOF) mass spectrometer for high-throughput label-free quantification with data-independent acquisition. The parallel accumulation-serial fragmentation (PASEF) operation mode positions the mass-selecting quadrupole as a function of the TIMS separation, which allows highly efficient data-independent acquisition schemes (dia-PASEF), but also increases complexity in the method design. We provide a step-by-step protocol for instrument setup, method design, data acquisition and ion mobility-aware, library-based data analysis with Spectronaut. We highlight key acquisition parameters and illustrate their optimization for short gradients. Using the EvosepOne liquid chromatography system, we demonstrate expected results for the analysis of a human cancer cell line at a throughput of 60 samples per day, leading to the quantification of about 6000 protein groups with very high reproducibility. Importantly, the protocol can be readily adapted to other gradients and sample types such as modified peptides.

Sodium adduct formation with graph-based machine learning can aid structural elucidation in non-targeted LC/ESI/HRMS

Non-targeted screening with LC/ESI/HRMS aims to identify the structure of the detected compounds using their retention time, exact mass, and fragmentation pattern. Challenges remain in differentiating between isomeric compounds. One untapped possibility to facilitate identification of isomers relies on different ionic species formed in electrospray. In positive ESI mode, both protonated molecules and adducts can be formed; however, not all isomeric structures form the same ionic species. The complicated mechanism of adduct formation has hindered the use of this molecular characteristic in the structural elucidation in non-targeted screening. Here, we have studied the adduct formation for 94 small molecules with ion mobility spectra and compared collision cross-sections of the respective ions. Based on the results we developed a fast support vector machine classifier with polynomial kernels for accurately predicting the sodium adduct formation in ESI/HRMS. The model is trained on five independent data sets from different laboratories and uses the graph-based connectivity of functional groups and PubChem fingerprints to predict the sodium adduct formation in ESI/HRMS. The validation of the model showed an accuracy of 74.7% (balanced accuracy 70.0%) on a dataset from an independent laboratory, which was not used in the training of the model. Lastly, we applied the classification algorithm to the SusDat database by NORMAN network to evaluate the proportion of isomeric compounds that could be distinguished based on predicted sodium adduct formation. It was observed that sodium adduct formation probability can provide additional selectivity for about one quarter of the exact masses and, therefore, shows practical utility for structural assignment in non-targeted screening.

Accelerating prototyping experiments for traveling wave structures for lossless ion manipulations

Traveling wave structures for lossless ion manipulation (TW-SLIM) has proven a valuable tool for the separation and study of gas-phase ions. Unfortunately, many of the traditional components of TW-SLIM experiments manifest practical and financial barriers to the technique's broad implementation. To this end, a series of technological innovations and methodologies are presented which enable for simplified SLIM experimentation and more rapid TW-SLIM prototyping. In addition to the use of multiple independent board sets that comprise the present SLIM system, we introduce a low-cost, multifunctional traveling wave generator to produce TW within the TW-SLIM. This square-wave producing unit proved effective in realizing TW-SLIM separations compared to traditional approaches. Maintaining a focus on lowering barriers to implementation, the present set of experiments explores the use of on-board injection (OBI) methods, which offer potential alternatives to ion funnel traps. These OBI techniques proved feasible and the ability of this simplified TW-SLIM platform to enhance ion accumulation was established. Further experimentation regarding ion accumulation revealed a complexity to ion accumulation within TW-SLIM that has yet to be expounded upon. Lastly, the ability of the presented TW-SLIM platform to store ions for extended periods (1 s) without significant loss (<10%) was demonstrated. The aforementioned experiments clearly establish the efficacy of a simplified TW-SLIM platform which promises to expand adoption and experimentation of the technique.

Spatial lipidomics of eight edible nuts by desorption electrospray ionization with ion mobility mass spectrometry imaging

Nuts have long been known for their health benefits which are mainly contributed by their lipid components. However, the spatial distribution of lipids in nuts has not been firmly established. In this study, desorption electrospray ionization combined with ion mobility and quadrupole time-of-flight mass spectrometry in positive and negative ion modes was applied to visualize spatially the lipids in eight edible nuts, namely almonds, hazelnuts, cashews, walnuts, peanuts, peach seeds, bitter almonds, and Chinese dwarf cherry seeds. The glycerophospholipids were first imaged in nuts in the negative ion mode, while the glycerolipids and phosphatidylcholines were mainly detected in the positive ion mode. In total 87 characterized components, including 47 glycerophospholipids, 24 glycerolipids, eight alkyl phenolic acids, three fatty acid acyl metabolites, four oligosaccharides, and amygdalin, were visualized in the eight nuts, and the collision cross-sectional values of these components were obtained. The outer shell of the nut cotyledon concentrated more abundant components than the center, while for the hydrolyzed glycerophospholipids, the reverse was observed. The results provide a more comprehensive and in-depth understanding of the location of the diverse metabolite profiles in nuts and of their relationship to their respective health benefits.

Rapid HILIC-Z ion mobility mass spectrometry (RHIMMS) method for untargeted metabolomics of complex biological samples

INTRODUCTION

Recent advances in high-throughput methodologies in the 'omics' and synthetic biology fields call for rapid and sensitive workflows in the metabolic phenotyping of complex biological samples.

OBJECTIVE

The objective of this research was to evaluate a straightforward to implement LC-MS metabolomics method using a commercially available chromatography column that provides increased throughput. Reducing run time can potentially impact chromatography and therefore the effects of ion mobility spectrometry to expand peak capacity were also evaluated. Additional confidence provided via collision cross section measurements for detected features was also explored.

METHODS

A rapid untargeted metabolomics workflow was developed with broad metabolome coverage, combining zwitterionic-phase hydrophilic interaction chromatography (HILIC-Z) with drift tube ion mobility-quadrupole time-of-flight (DTIM-qTOF) mass spectrometry. The analytical performance of our method was explored using extracts from complex biological samples, including a reproducibility study on chicken serum and a simple comparative study on a bacterial metabolome.

RESULTS

The method is acronymised RHIMMS for rapid HILIC-Z ion mobility mass spectrometry. We present the RHIMMS workflow starting with data acquisition, followed by data processing and analysis. RHIMMS demonstrates improved chromatographic separation for a selection of metabolites with wide physicochemical properties while maintaining reproducibility at better than 20% over 200 injections at 3.5 min per sample for the selected metabolites, and a mean of 13.9% for the top 50 metabolites by intensity. Additionally, the combination of rapid chromatographic separation with ion mobility allows improved annotation and the ability to distinguish isobaric compounds.

CONCLUSION

Our results demonstrate RHIMMS to be a rapid, reproducible, sensitive and high-resolution analytical platform that is highly applicable to the untargeted metabolomics analysis of complex samples.

Separation of phosphorothioated oligonucleotide diastereomers using multiplexed drift tube ion mobility mass spectrometry

Hydrophilic interaction liquid chromatography (HILIC) coupled to drift tube ion mobility spectrometry (DTIMS) was used to separate diastereomers of five-unit oligonucleotides containing 0, 1, 2 or 3 phosphorothioate (PS) linkages. Multiplexed DTIMS (where ions are pulsed into the drift tube according to a pre-encoded sequence) and post-acquisition processing using an innovative demultiplexing tool were investigated. The electric field inside the drift tube was optimized to achieve the highest resolving power. The entrance voltage providing the best two-peak resolution was -1000V with 3-bit multiplexing. Under optimized conditions, the eight diastereomers of an oligonucleotide with three PS linkages (5'-TC∗G∗T∗G-3') could be separated unambiguously. Indeed, those diastereomers differed in their collision cross section (CCS) values. The minimal CCS values difference between two adjacent diastereomers was 0.9% with maximal RSD on CCS values of 0.3%. The use of multiplexed ion mobility and the novel high-resolution demultiplexing tool represents a real breakthrough for resolution enhancement of diastereomers in linear DTIMS.

Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS

Co-immunoprecipitation of proteins coupled to mass spectrometry is critical for the understanding of protein interaction networks. In instances where a suitable antibody is not available, it is common to graft synthetic tags onto a target protein sequence thereby allowing the use of commercially available antibodies for affinity purification. A common approach is through FLAG-Tag co-immunoprecipitation. To allow the selective elution of protein complexes, competitive displacement using a large molar excess of the tag peptides is often carried out. Yet, this creates downstream challenges for the mass spectrometry analysis due to the presence of large quantities of these peptides. Here, we demonstrate that Field Asymmetric Ion Mobility Spectrometry (FAIMS), a gas phase ion separation device prior to mass spectrometry analysis can be applied to FLAG-Tag co-immunoprecipitation experiments to increase the depth of protein coverage. By excluding these abundant tag peptides, we were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without the need for additional sample handling or altering sample preparation protocols. SIGNIFICANCE: We have shown that application of FAIMS separation in the gas phase can increase the proteome coverage of Flag-Tagged co-immunoprecipitation mass spectrometry experiments versus one without FAIMS. We were able to observe deeper coverage of interacting proteins and as a result, deeper biological insights, without additional sample handling, fractionation, machine run time or modifying the sample preparation protocol.

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

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

Recent technological developments for native mass spectrometry

Native mass spectrometry (MS), the analysis of proteins and protein complexes from solutions that stabilize native solution structures, is a rapidly expanding area. There is strong evidence supporting the retention of proteins' native folds in the absence of solvent under the experimental timescales of MS experiments. Therefore, instrumentation has been developed to use gas-phase native-like protein ions to exploit the speed, sensitivity, and selectivity of mass spectrometry approaches to solve emerging problems in structural biology. This article reviews some of the recent advances and applications in gas-phase instrumentation for structural proteomics.

Comparison of one-phase and two-phase extraction methods for porcine tissue lipidomics applying a fast and reliable tentative annotation workflow

Lipidomics has great potential for the discovery of biomarkers, elucidation of metabolic processes and identifying dysregulations in complex biological systems. Concerning biofluids like plasma or cerebrospinal fluid, several studies for the comparison of lipid extraction solvents have already been conducted. With respect to tissues, which can differ significantly in terms of dry matter content and composition, only few studies are available. The proper selection of an extraction method that covers the complexity and individuality of different tissues is challenging. The goal of this work was to provide a systematic overview on the potential of different extraction methods for a broad applicability. This study covers six different extraction procedures and four different reconstitution solvents applied to ten different porcine tissues. To get an overview of the individual lipid profiles, a workflow was developed for a fast and reliable tentative lipid annotation. Therefore, several machine learning tools were utilized, like the prediction of collision cross sections to support the tentative lipid identification in case of untargeted lipidomics. In terms of data evaluation, unsupervised (e.g. principal component analysis) and supervised (e.g. partial least square - discriminant analysis) methods were applied to visualize and subsequently interpret all generated information. Furthermore, the influence of the tissue composition on the extraction performance was investigated. It could be shown that the ten porcine tissues can be distinguished based on their lipid profile with the applied workflow and that the methyl-tert-butyl ether (MTBE) based extraction method (two-phase) showed the best overall performance for the 16 examined lipid species. With this method the highest number of features (428 in lung tissue) could be annotated. Upcoming one-phase extractions also showed a high potential concerning total number of extracted lipids. Methanol/MTBE/chloroform (MMC) extracted slightly less lipids (393 in lung and liver) than MTBE but turned out to be the best one-phase extraction method. Additionally, the numbers of extracted lipids obtained by isopropanol/water 90:10 (IPA90) (399 in stomach) and by isopropanol/methanol/chloroform (IMC) (395 in stomach) were similar to those of the modified Folch method (402 in stomach). One-phase extractions can therefore clearly be seen as preferable when a high throughput is needed.

Identification of N-glycans with GalNAc-containing antennae from recombinant HIV trimers by ion mobility and negative ion fragmentation

Negative ion collision-induced dissociation (CID) of underivatized N-glycans has proved to be a simple, yet powerful method for their structural determination. Recently, we have identified a series of such structures with GalNAc rather than the more common galactose capping the antennae of hybrid and complex glycans. As part of a series of publications describing the negative ion fragmentation of different types of N-glycan, this paper describes their CID spectra and estimated nitrogen cross sections recorded by travelling wave ion mobility mass spectrometry (TWIMS). Most of the glycans were derived from the recombinant glycoproteins gp120 and gp41 from the human immunodeficiency virus (HIV), recombinantly derived from human embryonic kidney (HEK 293T) cells. Twenty-six GalNAc-capped hybrid and complex N-glycans were identified by a combination of TWIMS, negative ion CID, and exoglycosidase digestions. They were present as the neutral glycans and their sulfated and α2→3-linked sialylated analogues. Overall, negative ion fragmentation of glycans generates fingerprints that reveal their structural identity.

Boron nitride nanosheet-assisted matrix solid-phase dispersion microextraction of alkaloids from lotus plumule by high-performance liquid chromatography coupled with ultraviolet detection and ion mobility quadrupole time-of-flight mass spectrometry

A boron nitride nanosheet (BNNS)-assisted matrix solid-phase dispersion method was established to microextract alkaloids from medicinal plants. The target compounds were identified by high-performance liquid chromatography coupled with ultraviolet detection and ion mobility quadrupole time-of-flight mass spectrometry. During the experimental process, several important parameters, including the type of dispersant, the amount of dispersant, the grinding time, and the type of elution solvent, were optimized. Finally, the BNNSs were chosen as the best dispersant, and their microcosmic morphologies were identified by scanning electron microscopy and transmission electron microscopy. Because of the special property of BNNSs, the cost of this experiment was greatly reduced, especially in elution volume, sample amount (50 mg), and extraction time (2 min). Under the best conditions, 50 mg of sample powder was dispersed with 50 mg of BNNSs, the grinding time was 120 s, the mixed powder was eluted with 200 μL of methanol, and good linearity (r²  > 0.9993) and satisfactory recoveries (80-100%) were obtained. The inter- and intraday precisions were acceptable, with RSDs lower than 2.01 and 4.84%, respectively. The limits of detection ranged from 2.54 to 15.00 ng/mL, and the limits of quantitation were 8.47 to 50.00 ng/mL. The proposed method was successfully applied for the determination of liensinine, isoliensinine, and neferine in lotus plumule.

Predicting ion mobility as a function of the electric field for small ions in light gases

High resolution mobility devices such as Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) and Differential Mobility spectrometers (DMS) use strong electric fields to gas concentration ratios, E/N, to separate ions in the gas phase. While extremely successful, their empirical results show a non-linear, ion-dependent relation between mobility K and E/N that is difficult to characterize. The one-temperature theory Mason-Schamp equation, which is the most widely used ion mobility equation, unfortunately, cannot capture this behavior. When the two-temperature theory is used, it can be shown that the K-E/N behavior can be followed quite closely numerically by equating the effect of increasing the field to an increase in the ion temperature. This is attempted here for small ions in a Helium gas environment showing good agreement over the whole field range. To improve the numerical characterization, the Lennard-Jones (L-J) potentials may be optimized. This is attempted for Carbon, Hydrogen, Oxygen and Nitrogen at different degrees of theory up to the fourth approximation, which is assumed to be exact. The optimization of L-J improves the accuracy yielding errors of about 3% on average. The fact that a constant set of L-J potentials work for the whole range of E/N and for several molecules, also suggests that inelastic collisions can be circumvented in calculations for He. The peculiar K-E/N hump behaviors are studied, and whether mobility increases or decreases with E/N is shown to derive from a competition between relative kinetic energy and the interaction potentials.

Distinction of chiral penicillamine using metal-ion coupled cyclodextrin complex as chiral selector by trapped ion mobility-mass spectrometry and a structure investigation of the complexes

Penicillamine (Pen) is a common chiral drug that is obtained from penicillin. Between the two enantiomers of Pen, only D-Pen can be used to treat cystinuria and rheumatoid arthritis while L-Pen is toxic. Therefore, it requires great efforts for the research of the rigorous analysis and distinction of the two enantiomers. The non-covalent combination of chiral molecules and chiral selectors (CSs) has been proved as a unique strategy for chiral distinction by ion mobility spectrometry in coupling with -mss spectrometry (IM-MS). Here, we developed a simple method to distinguish D, L-Pen by using special CSs for IM-MS separation. The CSs utilized here include cyclodextrins (CD) and linear chain oligosaccharides plus metal ions. We found that non-covalent complexes [Pen+β-CD + Li]⁺ could be easily formed by electrospray ionization of the mixture of the solution, and the chirality of Pen could be effectively recognized by measuring their mobilities due to the different collision cross collision sections of [D-Pen+β-CD + Li]⁺ and [L-Pen+β-CD + Li]⁺. A detailed analysis of [Pen+β-CD + Li]⁺ was then conducted by the optical rotation measurements and NMR experiments to reveal their structural differences. Furthermore, DFT calculation showed the differences of molecular conformation between the complexes. The results provide a new powerful method for fast analysis and recognition of chirality of Pen compounds by IM-MS.

The relevant role of ion mobility separation in LC-HRMS based screening strategies for contaminants of emerging concern in the aquatic environment

Ion mobility separation (IMS) coupled to high resolution mass spectrometry (IMS-HRMS) is a promising technique for (non-)target/suspect analysis of micropollutants in complex matrices. IMS separates ionized compounds based on their charge, shape and size facilitating the removal of co-eluting isomeric/isobaric species. Additionally, IMS data can be translated into collision cross-section (CCS) values, which can be used to increase the identification reliability. However, IMS-HRMS for the screening of contaminants of emerging concern (CECs) have been scarcely explored. In this study, the role of IMS-HRMS for the identification of CECs in complex matrices is highlighted, with emphasis on when and with which purpose is of use. The utilization of IMS can result in much cleaner mass spectra, which considerably facilitates data interpretation and the obtaining of reliable identifications. Furthermore, the robustness of IMS measurements across matrices permits the use of CCS as an additional relevant parameter during the identification step even when reference standards are not available. Moreover, an effect on the number of true and false identifications could be demonstrated by including IMS restrictions within the identification workflow. Data shown in this work is of special interest for environmental researchers dealing with the detection of CECs with state-of-the-art IMS-HRMS instruments.

Comprehensive strategy for pesticide residue analysis in cocoa beans through qualitative and quantitative approach

Multiresidue quantitative and qualitative screening method for the analysis of pesticide residues in dried cocoa beans was validated and applied to imported and domestic cocoa beans samples. The quantitative method comprises of 15 pesticides while the screening method covers 110 pesticides of different chemical classes. The method was based on modified QuEChERS (Quick Easy Cheap Efficient Rugged Safe) extraction and detection using triple quadrupole (QQQ-MS) and ion mobility quadrupole time of flight mass spectrometry (IMS-QTOF). The method was quantitatively validated in terms of linearity, limit of quantification (LOQ), specificity, selectivity, accuracy, and precision. On the other hand, screening detection limits were established for 110 pesticides. Finally, the optimized strategy was successfully applied for the routine analysis of pesticide residues in 137 cocoa bean samples and 32% of the total samples were found positive for ametryn, chlorpyrifos, isoprocarb, and metalaxyl.

Wide-scope screening of pharmaceuticals, illicit drugs and their metabolites in the Amazon River

Only a limited number of households in the Amazon are served by sewage collection or treatment facilities, suggesting that there might be a significant emission of pharmaceuticals and other wastewater contaminants into freshwater ecosystems. In this work, we performed a wide-scope screening to assess the occurrence of pharmaceuticals, illicit drugs and their metabolites in freshwater ecosystems of the Brazilian Amazon. Our study included 40 samples taken along the Amazon River, in three of its major tributaries, and in small tributaries crossing four important urban areas (Manaus, Santarém, Macapá, Belém). More than 900 compounds were investigated making use of target and suspect screening approaches, based on liquid chromatography coupled to high-resolution mass spectrometry with ion mobility separation. Empirical collision-cross section (CCS) values were used to help and confirm identifications in target screening, while in the suspect screening approach CCS values were predicted using Artificial Neural Networks to increase the confidence of the tentative identification. In this way, 51 compounds and metabolites were identified. The highest prevalence was found in streams crossing the urban areas of Manaus, Macapá and Belém, with some samples containing up to 30 - 40 compounds, while samples taken in Santarém showed a lower number (8 - 11), and the samples taken in the main course of the Amazon River and its tributaries contained between 1 and 7 compounds. Most compounds identified in areas with significant urban impact belonged to the analgesics and antihypertensive categories, followed by stimulants and antibiotics. Compounds such as caffeine, cocaine and its metabolite benzoylecgonine, and cotinine (the metabolite of nicotine), were also detected in areas with relatively low anthropogenic impact and showed the highest total prevalence. This study supports the need to improve the sanitation system of urban areas in the Brazilian Amazon and the development of follow-up studies aimed at quantifying exposure levels and risks for Amazonian freshwater biodiversity.

The migration of NIAS from ethylene-vinyl acetate corks and their identification using gas chromatography mass spectrometry and liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry

An exhaustive migration study of eight corks, made of ethylene-vinyl acetate, was carried out to identify any non-volatile and volatile compounds using an untargeted approach. The challenge associated with the structural elucidation of unknowns was undertaken using both ultra-high-performance liquid chromatography coupled to an ion-mobility separation quadrupole-time of flight mass spectrometer and gas chromatography mass spectrometry. A total of fifty compounds were observed to migrate from the corks, and among these additives such as antioxidants (Butyl 4-hydroxybenzoate, Irganox 1010, Irganox 1075, Irgafos 168 and BHT) or lubricants (EBO and octadecanamide, N,N'-1,2-ethanediylbis-) were identified. A high proportion (84%) of the detected compounds was non-intentionally added substances (NIAS), and included several cyclic oligomers with different chain sequences. NIAS, such as 2,6-bis(1,1-dimethylethyl)-4-ethyl and 7,9-ditert-butyl-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione, break-down products, including hexa-, hepta- and nonadecanamide, N,N'-1,2-ethanediylbis-, and oxidation products were also identified. One cork was found to be unsuitable for use as a food contact material.

A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens

Background

The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow assays, each with their own strengths and weaknesses, have been developed and deployed in a short time.

Methods

Here, we describe an immunoaffinity purification approach followed a by high resolution mass spectrometry-based targeted qualitative assay capable of detecting SARS-CoV-2 viral antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data.

Findings

The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922–0.997) (86/88) sensitivity and 100% (95% CI = 0.958–1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method.

Interpretation

Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures.

Volatile organic compounds sensing based on Bennet doubler-inspired triboelectric nanogenerator and machine learning-assisted ion mobility analysis

Ion mobility analysis is a well-known analytical technique for identifying gas-phase compounds in fast-response gas-monitoring systems. However, the conventional plasma discharge system is bulky, operates at a high temperature, and inappropriate for volatile organic compounds (VOCs) concentration detection. Therefore, we report a machine learning (ML)-enhanced ion mobility analyzer with a triboelectric-based ionizer, which offers good ion mobility selectivity and VOC recognition ability with a small-sized device and non-strict operating environment. Based on the charge accumulation mechanism, a multi-switched manipulation triboelectric nanogenerator (SM-TENG) can provide a direct current (DC) bias at the order of a few hundred, which can be further leveraged as the power source to obtain a unique and repeatable discharge characteristic of different VOCs, and their mixtures, with a special tip-plate electrode configuration. Aiming to tackle the grand challenge in the detection of multiple VOCs, the ML-enhanced ion mobility analysis method was successfully demonstrated by extracting specific features automatically from ion mobility spectrometry data with ML algorithms, which significantly enhance the detection ability of the SM-TENG based VOC analyzer, showing a portable real-time VOC monitoring solution with rapid response and low power consumption for future internet of things based environmental monitoring applications.

Non-covalent double bond sensors for gas-phase infrared spectroscopy of unsaturated fatty acids

The position and configuration of carbon-carbon double bonds in unsaturated fatty acids is crucial for their biological functions and influences health and disease. However, double bond isomers are not routinely distinguished by classical mass spectrometry workflows. Instead, they require sophisticated analytical approaches usually based on chemical derivatization and/or instrument modification. In this work, a novel strategy to investigate fatty acid double bond isomers (18:1) without prior chemical treatment or modification of the ion source was implemented by non-covalent adduct formation in the gas phase. Fatty acid adducts with sodium, pyridinium, trimethylammonium, dimethylammonium, and ammonium cations were characterized by a combination of cryogenic gas-phase infrared spectroscopy, ion mobility-mass spectrometry, and computational modeling. The results reveal subtle differences between double bond isomers and confirm three-dimensional geometries constrained by non-covalent ion-molecule interactions. Overall, this study on fatty acid adducts in the gas phase explores new avenues for the distinction of lipid double bond isomers and paves the way for further investigations of coordinating cations to increase resolution.

The clinical potential of prm-PASEF mass spectrometry

INTRODUCTION

The continuous technical improvement in sensitivity and specificity placed mass spectrometry as an alternative method for analyzing clinical samples. In parallel to the rapid development of discovery proteomics, targeted acquisition has been implemented as a complementary option for measuring a small set of proteins with high sensitivity and robustness in a large sample cohort. The combination of trapped ion mobility with a rapid time-of-flight (TOF) mass spectrometer improves the sensitivity even further and triggers the development of prm-PASEF.

AREAS COVERED

This article discusses the development of prm-PASEF and its advantages over the existing targeted and discovery methods for analyzing clinical samples. We are also highlighting the different requirements for the use of prm-PASEF on clinical samples.

EXPERT OPINION

prm-PASEF takes advantage of a dual ion-mobility trap enabling highly multiplexed targeted acquisition. It allows the implementation of a short chromatographic separation setup without sacrificing the number of targeted peptides. Analyzing clinical samples by prm-PASEF holds the promise to significantly improve throughput while maintaining sensitivity to detect the selected target proteins.

Discrimination of isomeric monosaccharide derivatives using collision-induced fingerprinting coupled to ion mobility mass spectrometry

Because of the isomeric heterogeneity that is ubiquitous in analytical science, a formidable analytical challenge is to fully discriminate multiple isomers, especially those candidate isomers with various biological functions. Ion mobility mass spectrometry (IM-MS) has gained impressive advances for gaining molecular conformations, whereas coexisting structurally similar isomers often make unambiguous discrimination impossible due to the limited IM resolution of commercially available instruments. Herein, we demonstrate an energy-resolved collision-induced fingerprint (CIF) method to fully discriminate isomeric monosaccharide derivatives that differ in terms of composition, connectivity and configuration without complex instrument modifications. By simply increasing the collisional energy in the trap cell, the full width at half maximum (FWHM) of IM peaks can be markedly narrowed by at least 2-fold. Given the excellent reproducibility of CIF measurements, the full discrimination of isomers can benefit from their unique feature values and root-mean square deviation (RMSD) in CIF spectra. Moreover, rapid discrimination of each monosaccharide derivate isomer from binary mixtures is demonstrated. This strategy will expand the horizons of IM-MS platform in the rapid differentiation of a wider range of isomers more than monosaccharide derivatives in complex systems, which facilitates the identification and evaluation of innovative isomer candidates with unexplored functions.

Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry

Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.

Hexa-cata-hexabenzocoronene nanographene as a promising anode material for Mg-ion batteries

We investigated the possible use of a hexa-cata-hexabenzocoronene nanographene (HCHN) as an anode material for Mg-ion batteries (MIBs) implementing the B3LYP-gCP-D3/6-31G* scheme. The Mg cation or atom is adsorbed on the HCHN with the adsorption energy of - 200.3 or - 4.7 kcal/mol. The energy barrier related to transferring Mg cation on the HCHN surface was calculated to be 7.5 kcal/mol, producing the diffusion coefficient of 1.90 × 10^-8 cm²/s. It shows that the ion mobility is high and the rate of charge or discharge is fast. The calculated specific storage capacity of HCHN is 589.4 mAh/g and the great cell voltage is 4.23 V that is generated by the interaction of cation-π between Mg²⁺ and HCHN, which is strong. The HCHN is considered an ideal candidate to be used as an anode material in MIBs since its storage capacity and ion mobility are high, and it has a large cell voltage.

Aptamer-ligand recognition studied by native ion mobility-mass spectrometry

The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.

The use of UHPLC, IMS, and HRMS in multiresidue analytical methods: A critical review

Residue chemists who analyse pesticides in vegetables or veterinary drugs in animal-based food are currently facing a situation where there is a requirement to detect more and more compounds at lower and lower concentrations. Conventional tandem quadrupole instruments provide sufficient sensitivity, but speed and selectivity appear as future limitations. This will become an even larger issue when there is a need to not only detect active compounds but also their degradation products and metabolites. This will likely lead to a situation in which the conventional targeted approach must be expanded or augmented by a certain non-targeted strategy. High-resolution mass spectrometry provides such capabilities, but it frequently requires an additional degree of selectivity for the unequivocal confirmation of analytes present at trace levels in highly complex and variable food matrices. The hyphenation of ultrahigh performance liquid chromatography with ion mobility and high-resolution mass spectrometry provides analytical chemists with a new tool for performing such a demanding multiresidue analysis. The objective of this paper is to investigate the benefits of the added ion mobility dimension as well as to critically discuss the current limitations of this commercially available technology.

Sphingolipid metabolism as a marker of hepatotoxicity in drug-induced liver injury

Drug-induced liver injury (DILI) has a substantial impact on human health and is a major monetary burden on the drug development process. Presently, there is a lack of robust and analytically validated markers for predicting and early diagnosis of DILI. Sphingolipid metabolism and subsequent disruption of sphingolipid homeostasis has been documented to play a key role contributing to hepatocellular death and subsequent liver injury. A more comprehensive understanding of sphingolipid metabolism in response to liver toxicity has great potential to gain mechanistic insight into hepatotoxicity and define molecular markers that are responsible for hepatocyte dysfunction. Here, we present an analytical platform that provides multidimensional mass spectrometry-based datasets for comprehensive structure characterization of sphingolipids extracted from human primary hepatocytes (HPH) exposed to toxic levels of acetaminophen (APAP). Sphingolipid metabolism as measured by characterization of individual sphingolipid structure was sensitive to APAP toxicity displaying a concentration-dependent response. A number of sphingolipid structures were differentially expressed across varying APAP exposures highlighting the unique role sphingolipid metabolism has in response to hepatotoxicity and its potential use as a molecular marker in DILI.

Evidence of conformational landscape alteration and macromolecular complex formation in the early stages of in vitro human prion protein oxidation

Oxidative stress is proposed to be one of the major causes of neurodegenerative diseases. Cellular prion protein (PrP) oxidation has been widely studied using chemical reagents such as hydrogen peroxide. However, the experimental conditions used do not faithfully reflect the physiological environment of the cell. With the goal to explore the conformational landscape of PrP under oxidative stress, we conducted a set of experiments combining the careful control of the nature and the amount of ROS produced by a⁶⁰Co γ-irradiation source. Characterization of the resulting protein species was achieved using a set of analytical techniques. Under our experimental condition hydroxyl radical are the main reactive species produced. The most important findings are i) the formation of molecular assemblies under oxidative stress, ii) the detection of a majority of unmodified monomer mixed with oxidized monomers in these molecular assemblies at low hydroxyl radical concentration, iii) the absence of significant oxidation on the monomer fraction after irradiation. Molecular assemblies are produced in small amounts and were shown to be an octamer. These results suggest either i) an active recruitment of intact monomers by molecular assemblies' oxidized monomers then inducing a structural change of their intact counterparts or ii) an intrinsic capability of intact monomer conformers to spontaneously associate to form stable molecular assemblies when oxidized monomers are present. Finally, abundances of the intact monomer conformers after irradiation were modified. This suggests that monomers of the molecular assemblies exchange structural information with intact irradiated monomer. All these results shed a new light on structural exchange information between PrP monomers under oxidative stress.