The application of ion mobility mass spectrometry to metabolomics

Development of a Platform for High-Resolution Ion Mobility Separations Coupled with Messenger Tagging Infrared Spectroscopy for High-Precision Structural Characterizations

The ability to uniquely identify a compound requires highly precise and orthogonal measurements. Here we describe a newly developed analytical platform that integrates high resolution ion mobility and cryogenic vibrational ion spectroscopy for high-precision structural characterizations. This platform allows for the temporal separation of isomeric/isobaric ions and provides a highly sensitive description of the ion's adopted geometry in the gas phase. The combination of these orthogonal structural measurements yields precise descriptors that can be used to resolve between and confidently identify highly similar ions. The unique benefits of our instrument, which integrates a structures for lossless ion manipulations ion mobility (SLIM IM) device with messenger tagging infrared spectroscopy, include the ability to perform high-resolution ion mobility separations and to record the IR spectra of all ions simultaneously. The SLIM IM device, with its 13 m separation path length, allows for multipass experiments to be performed for increased resolution as needed. It is integrated with an Agilent qTOF MS where the collision cell was replaced with a cryogenically held (30 K) TW-SLIM module. The cryo-SLIM is operated in a novel manner that allows ions to be streamed through the device and collisionally cooled to a temperature where they can form noncovalently bound N2 complexes that are maintained as they exit the device and are detected by the TOF mass analyzer. The instrument can be operated in two modes: IMS+IR where the IR spectra for mobility-selected ions can be recorded and IR-only mode where the IR spectra for all mass-resolved ions can be recorded. In IR-only mode, IR spectra (400 cm-1 spectral range) can be recorded in as short as 2 s for high throughput measurements. This work details the construction of the instrument and modes of operation. It provides initial benchmarking of CCS and IR measurements to demonstrate the utility of this instrument for targeted and untargeted approaches.

Matrix free laser desorption ionization coupled to trapped ion mobility mass spectrometry: an innovative approach for isomer differentiation and molecular network visualization

The chemical profiling of complex mixtures of natural products (NPs) is a major challenge in analytical chemistry and generally addressed by liquid chromatography coupled to mass spectrometry (LC-MS). In recent years also matrix free laser desorption ionization-mass spectrometry (LDI-MS) has become a versatile and time efficient complement to LC-MS. However, the absence of chromatographic separation in LDI-MS does not permit the differentiation of isomers. Providing a potential solution to this problem, the current work presents a combined LDI-Ion mobility spectrometry-tandem mass spectrometry (LDI-IMS-MS2) approach, which facilitated the successful differentiation of four constitutional xanthone isomers namely butyraxanthone D, cratoxylone, garcinone D and parvixanthone G. In addition, the experimental collision cross section (CCS) distribution values of nine unreported xanthones are described. Based on these results, a proof of concept for the so far unexplored concept of a LDI-IMS-MS2 based molecular network is being presented.

Rounded Turn SLIM Design for High-Resolution Ion Mobility Mass Spectrometry Analysis of Small Molecules

Various rounded turn designs in Structures for Lossless Ion Manipulation (SLIM) were explored via ion trajectory simulations. The optimized design was integrated into a SLIM ion mobility (IM) system coupled with a time-of-flight (TOF) mass spectrometer (MS) for further experimental investigation. The SLIM-TOF IM-MS system was assessed for IM resolution and ion transmission efficiency across a wide m/z range using various RF frequencies and buffer gas combinations. High ion transmission efficiency and high resolution ion mobility (HRIM) separation were achieved for Agilent tune mix ions through a ∼12.8 m serpentine separation path in both nitrogen and helium. In helium, ion transmission for low m/z ions was enhanced at higher RF trapping frequency, enabling the detection of ions with m/z below 50 and all 17 amino acids from a standard mixture. Lossless ion transmission was observed for glycine (m/z 76) in both passthrough and HRIM modes. HRIM resolution was benchmarked using L-isoleucine, L-leucine, and various other isobaric and isomeric metabolites with m/z values of 60-89. This work demonstrates a rounded turn SLIM design that enables HRIM measurements for small molecule analytes, with a particular focus on metabolomics, where IM offers a means to enhance the speed, robustness, and specificity of analytical workflows.

Advances in mass spectrometry for metabolomics: Strategies, challenges, and innovations in disease biomarker discovery

Mass spectrometry (MS) plays a crucial role in metabolomics, especially in the discovery of disease biomarkers. This review outlines strategies for identifying metabolites, emphasizing precise and detailed use of MS techniques. It explores various methods for quantification, discusses challenges encountered, and examines recent breakthroughs in biomarker discovery. In the field of diagnostics, MS has revolutionized approaches by enabling a deeper understanding of tissue-specific metabolic changes associated with disease. The reliability of results is ensured through robust experimental design and stringent system suitability criteria. In the past, data quality, standardization, and reproducibility were often overlooked despite their significant impact on MS-based metabolomics. Progress in this field heavily depends on continuous training and education. The review also highlights the emergence of innovative MS technologies and methodologies. MS has the potential to transform our understanding of metabolic landscapes, which is crucial for disease biomarker discovery. This article serves as an invaluable resource for researchers in metabolomics, presenting fresh perspectives and advancements that propels the field forward.

Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems

Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.

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.

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.

The Role of Ion Rotation in Ion Mobility: Ultrahigh-Precision Prediction of Ion Mobility Dependence on Ion Mass Distribution and Translational to Rotational Energy Transfer

The role of ion rotation in determining ion mobilities is explored using the subtle gas phase ion mobility shifts based on differences in ion mass distributions between isotopomer ions that have been observed with ion mobility spectrometry (IMS) measurements. These mobility shifts become apparent for IMS resolving powers on the order of ∼1500 where relative mobilities (or alternatively momentum transfer collision cross sections; Ω) can be measured with a precision of ∼10 ppm. The isotopomer ions have identical structures and masses, differing only in their internal mass distributions, and their Ω differences cannot be predicted by widely used computational approaches, which ignore the dependence of Ω on the ion's rotational properties. Here, we investigate the rotational dependence of Ω, which includes changes to its collision frequency due to thermal rotation as well as the coupling of translational to rotational energy transfer. We show that differences in rotational energy transfer during ion-molecule collisions provide the major contribution to isotopomer ion separations, with only a minor contribution due to an increase in collision frequency due to ion rotation. Modeling including these factors allowed for differences in Ω to be calculated that precisely mirror the experimental separations. These findings also highlight the promise of pairing high-resolution IMS measurements with theory and computation for improved elucidation of subtle structural differences between ions.

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.

Metabolomics during the spontaneous fermentation in cocoa (Theobroma cacao L.): An exploraty review

Spontaneous fermentation is a process that depends on substrates' physical characteristics, crop variety, and postharvest practices; it induces variations in the metabolites that are responsible for the taste, aroma, and quality. Metabolomics makes it possible to detect key metabolites using chemometrics and makes it possible to establish patterns or identify biomarker behaviors under certain conditions at a given time. Therefore, sensitive and highly efficient analytical techniques allow for studying the metabolomic fingerprint changes during fermentation; which identify and quantify metabolites related to taste and aroma formation of an adequate processing time. This review shows that studying metabolomics in spontaneous fermentation permits the characterization of spontaneous fermentation in different stages. Also, it demonstrates the possibility of modulating the quality of cocoa by improving the spontaneous fermentation time (because of volatile aromatic compounds formation), thus standardizing the process to obtain attributes and quality that will later impact the chocolate quality.

Food metabolomics: Latest hardware-developments for nontargeted food authenticity and food safety testing

The analytical requirements for food testing have increased significantly in recent years. On the one hand, because food fraud is becoming an ever-greater challenge worldwide, and on the other hand because food safety is often difficult to monitor due to the far-reaching trade chains. In addition, the expectations of consumers on the quality of food have increased, and they are demanding extensive information. Cutting-edge analytical methods are required to meet these demands. In this context, non-targeted metabolomics strategies using mass and nuclear magnetic resonance spectrometers (mass spectrometry [MS]) have proven to be very suitable. MS-based approaches are of particular importance as they provide a comparatively high analytical coverage of the metabolome. Accordingly, the efficiency to address even challenging issues is high. A variety of hardware developments, which are explained in this review, have contributed to these advances. In addition, the potential of future developments is highlighted, some of which are currently not yet commercially available or only used to a comparatively small extent but are expected to gain in importance in the coming years.

Metabolomics and modelling approaches for systems metabolic engineering

Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.

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.

Ion Mobility-Derived Collision Cross-Sections Add Extra Capability in Distinguishing Isomers and Compounds with Similar Retention Times: The Case of Aphidicolanes

The hyphenation of ion mobility spectrometry with high-resolution mass spectrometry has been widely used in the characterization of various metabolites. Nevertheless, such a powerful tool remains largely unexplored in natural products research, possibly mainly due to the lack of available compounds. To evaluate the ability of collision cross-sections (CCSs) in characterizing compounds, especially isomeric natural products, here we measured and compared the traveling-wave IMS-derived nitrogen CCS values for 75 marine-derived aphidicolanes. We established a CCS database for these compounds which contained 227 CCS values of different adducts. When comparing the CCS differences, 36 of 57 pairs (over 60%) of chromatographically neighboring compounds showed a ΔCCS over 2%. What is more, 64 of 104 isomeric pairs (over 60%) of aphidicolanes can be distinguished by their CCS values, and 13 of 18 pairs (over 70%) of chromatographically indistinguishable isomers can be differentiated from the mobility dimension. Our results strongly supported CCS as an important parameter with good orthogonality and complementarity with retention time. CCS is expected to play an important role in distinguishing complex and diverse marine natural products.

Structural characterization and analysis of different epimers of neutral glycosphingolipid LcGg4 by ion mobility spectrometry-mass spectrometry

LcGg4, a neutral glycosphingolipid (GSL) and cancer antigen, its epimers GalNAc-LcGg4 and GlcNAc-LcGg4, and three lipid forms of GalNAc-LcGg4 were studied by mass spectrometry (MS). It was found that different forms of GalNAc-LcGg4 carrying homologous (d16:1/18:0) and (d18:1/18:0) lipids were easily separated and identified using liquid chromatography (LC)-MS. In addition, like gangliosides, homologous lipid forms of GalNAc-LcGg4 showed the same fragmentation pattern, except for a uniform shift of their glycolipid product ions by a certain m/z number determined by the varied lipid structure. It was also disclosed that LcGg4 and its epimers GalNAc-LcGg4 and GlcNAc-LcGg4, which are different only in the C4-configuration of their non-reducing end sugar residues, gave the same MS/MS product ions in similar relative intensities, as well as the same LC retention time, suggesting the challenge to differentiate epimeric GSLs by LC-MS. However, ion mobility spectrometry (IMS)-MS was able to efficiently separate and distinguish these epimers. This study has demonstrated the promise of IMS-MS for isomeric GSL characterization and the IMS-MS and LC-MS/MS combination for natural GSL analysis.

Application of MS-Based Metabolomic Approaches in Analysis of Starfish and Sea Cucumber Bioactive Compounds

Today, marine natural products are considered one of the main sources of compounds for drug development. Starfish and sea cucumbers are potential sources of natural products of pharmaceutical interest. Among their metabolites, polar steroids, triterpene glycosides, and polar lipids have attracted a great deal of attention; however, studying these compounds by conventional methods is challenging. The application of modern MS-based approaches can help to obtain valuable information about such compounds. This review provides an up-to-date overview of MS-based applications for starfish and sea cucumber bioactive compounds analysis. While describing most characteristic features of MS-based approaches in the context of starfish and sea cucumber metabolites, including sample preparation and MS analysis steps, the present paper mainly focuses on the application of MS-based metabolic profiling of polar steroid compounds, triterpene glycosides, and lipids. The application of MS in metabolomics studies is also outlined.

Evaluating the Effects of Metal Adduction and Charge Isomerism on Ion-Mobility Measurements using m-Xylene Macrocycles as Models

Gas-phase ion-mobility spectrometry provides a unique platform to study the effect of mobile charge(s) or charge location on collisional cross section and ion separation. Here, we evaluate the effects of cation/anion adduction in a series of xylene and pyridyl macrocycles that contain ureas and thioureas. We explore how zinc binding led to unexpected deprotonation of the thiourea macrocyclic host in positive polarity ionization and subsequently how charge isomerism due to cation (zinc metal) and anion (chloride counterion) adduction or proton competition among acceptors can affect the measured collisional cross sections in helium and nitrogen buffer gases. Our approach uses synthetic chemistry to design macrocycle targets and a combination of ion-mobility spectrometry mass spectrometry experiments and quantum mechanics calculations to characterize their structural properties. We demonstrate that charge isomerism significantly improves ion-mobility resolution and allows for determination of the metal binding mechanism in metal-inclusion macrocyclic complexes. Additionally, charge isomers can be populated in molecules where individual protons are shared between acceptors. In these cases, interactions via drift gas collisions magnify the conformational differences. Finally, for the macrocyclic systems we report here, charge isomers are observed in both helium and nitrogen drift gases with similar resolution. The separation factor does not simply increase with increasing drift gas polarizability. Our study sheds light on important properties of charge isomerism and offers strategies to take advantage of this phenomenon in analytical separations.

Assessing the Dipole Moments and Directional Cross Sections of Proteins and Complexes by Differential Ion Mobility Spectrometry

Ion mobility spectrometry (IMS) has become a mainstream approach to fractionate complex mixtures, separate isomers, and assign the molecular geometries. All modalities were grouped into linear IMS (based on the absolute ion mobility, K) and field asymmetric waveform IMS (FAIMS) relying on the evolution of K at a high normalized electric field (E/N) that induces strong ion heating. In the recently demonstrated low-field differential (LOD) IMS, the field is too weak for significant heating but locks the macromolecular dipoles to produce novel separations controlled by the relevant directional collision cross sections (CCSs). Here, we show LODIMS for mass-selected species, exploring the dipole alignment across charge states for the monomers and dimers of an exemplary protein, the alcohol dehydrogenase. Distinct conformational families for aligned species are revealed with directional CCS estimated from the field-dependent trend lines. We set up a model to extract the fractions of pendular conformers as a function of field intensity and translate them into dipole moment distributions. These developments make a critical step toward establishing LODIMS as a new tool for top-down proteomics and integrative structural biology.

Infrared Laser Ablation Microsampling with a Reflective Objective

A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm² area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm² were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.

Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses

While the combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments, ensuring these prioritized features originate from endogenous metabolism remains challenging. Isotopologue workflows, such as isotopic ratio outlier analysis (IROA), mass isotopomer ratio analysis of U-¹³C labeled extracts (MIRACLE), and credentialing incorporate isotopic labels directly into metabolic precursors, guaranteeing that all features of interest are unequivocal byproducts of cellular metabolism. Furthermore, comprehensive separation and annotation of small molecules continue to challenge the metabolomics field, particularly for isomeric systems. In this paper, we evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows. Since isotopically labeled molecules codrift in the IMS dimension with their ¹²C versions, LC-IMS-CID-MS provides four dimensions (LC, IMS, MS, and MS/MS) to directly investigate the metabolic activity of prioritized untargeted features. Here, we demonstrate this additional selectivity by showcasing how a preliminary data set of 30 endogeneous metabolites are putatively annotated from isotopically labeled Escherichia coli cultures when analyzed by LC-IMS-CID-MS. Metabolite annotations were based on several molecular descriptors, including accurate mass measurement, carbon number, annotated fragmentation spectra, and collision cross section (CCS), collectively illustrating the importance of incorporating IMS into isotopologue workflows. Overall, our results highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments.

Prediction of Collision Cross Section Values: Application to Non-Intentionally Added Substance Identification in Food Contact Materials

The synthetic chemicals in food contact materials can migrate into food and endanger human health. In this study, the traveling wave collision cross section in nitrogen values of more than 400 chemicals in food contact materials were experimentally derived by traveling wave ion mobility spectrometry. A support vector machine-based collision cross section (CCS) prediction model was developed based on CCS values of food contact chemicals and a series of molecular descriptors. More than 92% of protonated and 81% of sodiated adducts showed a relative deviation below 5%. Median relative errors for protonated and sodiated molecules were 1.50 and 1.82%, respectively. The model was then applied to the structural annotation of oligomers migrating from polyamide adhesives. The identification confidence of 11 oligomers was improved by the direct comparison of the experimental data with the predicted CCS values. Finally, the challenges and opportunities of current machine-learning models on CCS prediction were also discussed.

Recent Analytical Approaches for the Study of Bioavailability and Metabolism of Bioactive Phenolic Compounds

The study of the bioavailability of bioactive compounds is a fundamental step for the development of applications based on them, such as nutraceuticals, functional foods or cosmeceuticals. It is well-known that these compounds can undergo metabolic reactions before reaching therapeutic targets, which may also affect their bioactivity and possible applications. All recent studies that have focused on bioavailability and metabolism of phenolic and terpenoid compounds have been developed because of the advances in analytical chemistry and metabolomics approaches. The purpose of this review is to show the role of analytical chemistry and metabolomics in this field of knowledge. In this context, the different steps of the analytical chemistry workflow (design study, sample treatment, analytical techniques and data processing) applied in bioavailability and metabolism in vivo studies are detailed, as well as the most relevant results obtained from them.

Untargeted and Targeted LC-MS/MS Based Metabolomics Study on In Vitro Culture of Phaeoacremonium Species

Grapevine (Vitis vinifera L.) can be affected by many different biotic agents, including tracheomycotic fungi such as Phaeomoniella chlamydospora and Phaeoacremonium minimum, which are the main causal agent of Esca and Petri diseases. Both fungi produce phytotoxic naphthalenone polyketides, namely scytalone and isosclerone, that are related to symptom development. The main objective of this study was to investigate the secondary metabolites produced by three Phaeoacremonium species and to assess their phytotoxicity by in vitro bioassay. To this aim, untargeted and targeted LC-MS/MS-based metabolomics were performed. High resolution mass spectrometer UHPLC-Orbitrap was used for the untargeted profiling and dereplication of secondary metabolites. A sensitive multi reaction monitoring (MRM) method for the absolute quantification of scytalone and isosclerone was developed on a UPLC-QTrap. Different isolates of P. italicum, P. alvesii and P. rubrigenum were grown in vitro and the culture filtrates and organic extracts were assayed for phytotoxicity. The toxic effects varied within and among fungal isolates. Isosclerone and scytalone were dereplicated by matching retention times and HRMS and MS/MS data with pure standards. The amount of scytalone and isosclerone differed within and among fungal species. To our best knowledge, this is the first study that applies an approach of LC-MS/MS-based metabolomics to investigate differences in the metabolic composition of organic extracts of Phaeoacremonium species culture filtrates.

A Rapid and Sensitive Method for the Simultaneous Determination of Multipolar Compounds in Plant Tea by Supercritical Fluid Chromatography Coupled to Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry

In this study, matrix solid phase dispersion (MSPD) microextraction combined with supercritical fluid chromatography-ion mobility quadrupole time-of-flight mass spectrometry (SFC/IM-QTOF-MS) was used to analyze the multipolar compounds in plant tea. The parameters of stationary phase, mobile phase, make-up solution, temperature, and back pressure were optimized. The target analytes were gradient eluted in 8 min by supercritical CO₂ on a Zorbax RX-SIL column. Collisional Cross Section (CCS) values for single and multiple fields were measured. A series of validation studies were carried out under the optimal conditions, and the linear relationship and reproducibility were good. The limits of detection were 1.4 (Scoparone (1))~70 (Naringenin (4)) ng/mL, and the limits of quantification were 4.7 (Scoparone (1))~241 (Naringenin (4)) ng/mL. The recoveries of most compounds ranged from 60.7% to 127%. As a consequence, the proposed method was used for the separation and quantitative analysis of active ingredients in caulis dendrobii.

Food Metabolites as Tools for Authentication, Processing, and Nutritive Value Assessment

Secondary metabolites are molecules with unlimited applications that have been gaining importance in various industries and studied from many angles. They are mainly used for their bioactive capabilities, but due to the improvement of sensibility in analytical chemistry, they are also used for authentication and as a quality control parameter for foods, further allowing to help avoid food adulteration and food fraud, as well as helping understand the nutritional value of foods. This manuscript covers the examples of secondary metabolites that have been used as qualitative and authentication molecules in foods, from production, through processing and along their shelf-life. Furthermore, perspectives of analytical chemistry and their contribution to metabolite detection and general perspectives of metabolomics are also discussed.

Metabolomic Profiling of Human Urine Samples Using LC-TIMS-QTOF Mass Spectrometry

The identification of metabolites in biological samples is challenging due to their chemical and structural diversity. Ion mobility spectrometry (IMS) separates ionized molecules based on their mobility in a carrier buffer gas giving information about the ionic shape by measuring the rotationally averaged collision cross-section (CCS) value. This orthogonal descriptor, in combination with the m/z, isotopic pattern distribution, and MS/MS spectrum, has the potential to improve the identification of molecular molecules in complex mixtures. Urine metabolomics can reveal metabolic differences, which arise as a result of a specific disease or in response to therapeutic intervention. It is, however, complicated by the presence of metabolic breakdown products derived from a wide range of lifestyle and diet-related byproducts, many of which are poorly characterized. In this study, we explore the use of trapped ion mobility spectrometry (TIMS) via LC parallel accumulation with serial fragmentation (PASEF) for urine metabolomics. A total of 362 urine metabolites were characterized from 80 urine samples collected from healthy volunteers using untargeted metabolomics employing HILIC and RP chromatography. Additionally, three analytes (Trp, Phe, and Tyr) were selected for targeted quantification. Both the untargeted and targeted data was highly reproducible and reported CCS measurements for identified metabolites were robust in the presence of the urine matrix. A comparison of CCS values among different laboratories was also conducted, showing less than 1.3% ΔCCS values across different platforms. This is the first report of a human urine metabolite database compiled with CCS values experimentally acquired using an LC-PASEF TIMS-qTOF platform.

Multidimensional Separations of Intact Phase II Steroid Metabolites Utilizing LC-Ion Mobility-HRMS

The detection and unambiguous identification of anabolic-androgenic steroid metabolites are essential in clinical, forensic, and antidoping analyses. Recently, sulfate phase II steroid metabolites have received increased attention in steroid metabolism and drug testing. In large part, this is because phase II steroid metabolites are excreted for an extended time, making them a potential long-term chemical marker of choice for tracking steroid misuse in sports. Comprehensive analytical methods, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS), have been used to detect and identify glucuronide and sulfate steroids in human urine with high sensitivity and reliability. However, LC-MS/MS identification strategies can be hindered by the fact that phase II steroid metabolites generate nonselective ion fragments across the different metabolite markers, limiting the confidence in metabolite identifications that rely on exact mass measurement and MS/MS information. Additionally, liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is sometimes insufficient at fully resolving the analyte peaks from the sample matrix (commonly urine) chemical noise, further complicating accurate identification efforts. Therefore, we developed a liquid chromatography-ion mobility-high resolution mass spectrometry (LC-IM-HRMS) method to increase the peak capacity and utilize the IM-derived collision cross section (CCS) values as an additional molecular descriptor for increased selectivity and to improve identifications of intact steroid analyses at low concentrations.

Characterizing Multidevice Capillary Vibrating Sharp-Edge Spray Ionization for In-Droplet Hydrogen/Deuterium Exchange to Enhance Compound Identification

Multidevice capillary vibrating sharp-edge spray ionization (cVSSI) source parameters have been examined to determine their effects on conducting in-droplet hydrogen/deuterium exchange (HDX) experiments. Control experiments using select compounds indicate that the observed differences in mass spectral isotopic distributions obtained upon initiation of HDX result primarily from solution-phase reactions as opposed to gas-phase exchange. Preliminary studies have determined that robust HDX can only be achieved with the application of same-polarity voltage to both the analyte and the deuterium oxide reagent (D₂O) cVSSI devices. Additionally, a similar HDX reactivity dependence on the voltage applied to the D₂O device for various analytes is observed. Analyte and reagent flow experiments show that, for the multidevice cVSSI setup employed, there is a nonlinear dependence on the D₂O reagent flow rate; increasing the D₂O reagent flow by 100% results in only an ∼10-20% increase in deuterium incorporation for this setup. Instantaneous (subsecond) response times have been demonstrated in the initiation or termination of HDX, which is achieved by turning on or off the reagent cVSSI device piezoelectric transducer. The ability to distinguish isomeric species by in-droplet HDX is presented. Finally, a demonstration of a three-component cVSSI device setup to perform multiple (successive or in combination) in-droplet chemistries to enhance compound ionization and identification is presented and a hypothetical metabolomics workflow consisting of successive multidevice activation is briefly discussed.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.

The Pharmacometabodynamics of Gefitinib after Intravenous Administration to Mice: A Preliminary UPLC-IM-MS Study

The effects of intravenous gefitinib (10 mg/kg), an anilinoquinazoline thymidylate kinase inhibitor (TKI), selective for the epidermal growth factor receptor (EGFR), on the urinary metabotypes of mice were studied. We hypothesized that, in response to the administration of gefitinib, there might be significant changes in the excretion of many endogenous metabolites in the urine, which could be correlated with the plasma pharmacokinetics (PK) of the drug. In order to investigate this conjecture, urine from male C57 BL6 mice was collected before IV dosing (10 mg/kg) and at 0–3, 3–8, and 8–24 h post-dose. The samples were profiled by UPLC/IM/MS and compared with the profiles obtained from undosed control mice with the data analyzed using multivariate statistical analysis (MVA). This process identified changes in endogenous metabolites over time and these were compared with drug and drug metabolite PK and excretion. While the MVA of these UPLC/IM/MS data did indeed reveal time-related changes for endogenous metabolites that appeared to be linked to drug administration, this analysis did not highlight the presence of either the drug or its metabolites in urine. Endogenous metabolites affected by gefitinib administration were identified by comparison of mass spectral, retention time and ion mobility-derived collision cross section data (compared to authentic standards wherever possible). The changes in endogenous metabolites resulting from gefitinib administration showed both increases (e.g., tryptophan, taurocholic acid, and the dipeptide lysyl-arginine) and decreases (e.g., deoxyguanosine, 8-hydroxydeoxyguanosine, and asparaginyl-histidine) relative to the control animals. By 8–24 h, the post-dose concentrations of most metabolites had returned to near control values. From these studies, we conclude that changes in the amounts of endogenous metabolites excreted in the urine mirrored, to some extent, the plasma pharmacokinetics of the drug. This phenomenon is similar to pharmacodynamics, where the pharmacological effects are related to the drug concentrations, and by analogy, we have termed this effect “pharmacometabodynamics”.

Configuration of the ion exchange chromatography, hydrophilic interaction chromatography, and reversed-phase chromatography as off-line three-dimensional chromatography coupled with high-resolution quadrupole-Orbitrap mass spectrometry for the multicomponent characterization of Uncaria sessilifructus

Herbs represent complex chemical systems involving various primary and secondary metabolites that are featured by large spans of acid-base property, polarity, molecular mass, and content, etc., which thus poses great challenges to characterize the metabolites contained. Here, the combination of multiple-mechanism chromatography coupled with improved data-dependent-MS² acquisition (DDA-MS²) is presented as a strategy to support the deep metabolites characterization. Targeting Uncaria sessilifructus, a reputable medicinal herb containing alkaloids and triterpenic acids (TAs) as the main pharmacologically bioactive ingredients, a three-dimensional liquid chromatography (3D-LC) system was established by integrating ion exchange chromatography, hydrophilic interaction chromatography, and reversed-phase chromatography (IEC-HILIC-RPC). The first-dimensional chromatography, configuring a PhenoSphere SCX column eluted by methanol/20 mM ammonium acetate-0.05% formic acid in water, could well fractionate the total extract into two fractions (unretained ingredients and alkaloids). The subsequent HILIC using an XAmide column and RPC by a CSH Phenyl-Hexyl column achieved the sufficient resolution of the total TAs and total alkaloids, respectively. A polarity-switching precursor ions list-including DDA approach by Q-Orbitrap-MS enabled the high-efficiency, coverage-enhanced identification of alkaloids and TAs. This 3D-LC/Q-Orbitrap-MS system was validated as precise (RSD < 5% for intra-day/inter-day precision), Up to 308 components were separated from U. sessilifructus, and 128 thereof (including 85 alkaloids, 29 TAs, and 14 others) were identified or tentatively characterized, exhibiting superiority over the conventional one-dimensional LC/MS. Conclusively, 3D-LC/MS in an off-line mode can facilitate the flexible configuration of multiple chromatography to accomplish the fit-for-purpose characterization of the metabolites from an herbal extract or a biosample.

The Role of High-Resolution Analytical Techniques in the Development of Functional Foods

The approaches based on high-resolution analytical techniques, such as nuclear magnetic resonance or mass spectrometry coupled to chromatographic techniques, have a determining role in several of the stages necessary for the development of functional foods. The analyses of botanical extracts rich in bioactive compounds is one of the fundamental steps in order to identify and quantify their phytochemical composition. However, the compounds characterized in the extracts are not always responsible for the bioactive properties because they generally undergo metabolic reactions before reaching the therapeutic targets. For this reason, analytical techniques are also applied to analyze biological samples to know the bioavailability, pharmacokinetics and/or metabolism of the compounds ingested by animal or human models in nutritional intervention studies. In addition, these studies have also been applied to determine changes of endogenous metabolites caused by prolonged intake of compounds with bioactive potential. This review aims to describe the main types and modes of application of high-resolution analytical techniques in all these steps for functional food development.

An Improved Calibration Approach for Traveling Wave Ion Mobility Spectrometry: Robust, High-Precision Collision Cross Sections

The combination of ion-mobility (IM) separation with mass spectrometry (MS) has impacted global measurement efforts in areas ranging from food analysis to drug discovery. Reasons for the broad adoption of IM-MS include its significantly increased peak capacity, duty-cycle, and ability to reconstruct fragmentation data in parallel, all of which greatly enable the analyses of complex mixtures. More fundamentally, however, measurements of ion-gas molecule collision cross sections (CCSs) are used to support compound identification and quantitation efforts as well as study the structures of large biomolecules. As the first commercialized form of IM-MS, Traveling Wave Ion Mobility (TWIM) devices are operated at low pressures (∼3 mbar) and voltages, are relatively short (∼25 cm), and separate ions on a timescale of tens of milliseconds. These qualities make TWIM ideally suited for hybridization with MS. Owing to the complicated motion of ions in TWIM devices, however, IM transit times must be calibrated to enable CCS measurements. Applicability of these calibrations has hitherto been restricted to primarily singly charged small molecules and some classes of large, multiply charged ions under a significantly narrower range of instrument conditions. Here, we introduce and extensively characterize a dramatically improved TWIM calibration methodology. Using over 2500 experimental TWIM data sets, covering ions that span over 3.5 orders of magnitude of molecular mass, we demonstrate robust calibrations for a significantly expanded range of instrument conditions, thereby opening up new analytical application areas and enabling the expansion of high-precision CCS measurements for both existing and next-generation TWIM instrumentation.

Recent applications of ion mobility spectrometry in natural product research

Ion mobility spectrometry (IMS) is a rapid separation technique capable of extracting complementary structural information to chromatography and mass spectrometry (MS). IMS, especially in combination with MS, has experienced inordinate growth in recent years as an analytical technique, and elicited intense interest in many research fields. In natural product analysis, IMS shows promise as an additional tool to enhance the performance of analytical methods used to identify promising drug candidates. Potential benefits of the incorporation of IMS into analytical workflows currently used in natural product analysis include the discrimination of structurally similar secondary metabolites, improving the quality of mass spectral data, and the use of mobility-derived collision cross-section (CCS) values as an additional identification criterion in targeted and untargeted analyses. This review aims to provide an overview of the application of IMS to natural product analysis over the last six years. Instrumental aspects and the fundamental background of IMS will be briefly covered, and recent applications of the technique for natural product analysis will be discussed to demonstrate the utility of the technique in this field.

An emerging powerful technique for distinguishing isomers: Trapped ion mobility spectrometry time-of-flight mass spectrometry for rapid characterization of estrogen isomers

RATIONALE

Isomer metabolites are involved in metabolic pathways, and their characterization is essential but remains challenging even using high-performance analytical platforms. The addition of ion mobility prior to mass analysis can help to separate isomers. Here, the ability of a recently developed trapped ion mobility spectrometry system to separate metabolite isomers was examined.

METHODS

Three pairs of estrogen isomers were studied as a model of isomeric metabolites under both negative and positive electrospray ionization (ESI) modes using a commercial trapped ion mobility spectrometry-TOF mass spectrometer. The standard metabolites were also spiked into human urine to evaluate the efficiency of trapped ion mobility spectrometry to separate isomers in complex mixtures.

RESULTS

The estradiol glucuronide isomers (E₂ β-3G and E₂ β-17G) could be distinguished as deprotonated species, while the estradiol epimers (E₂ β and E₂ α) and the methoxyestradiol isomers (2-MeO-E₂ β and 4-MeO-E₂ β) were separated as lithiated adducts in positive ionization mode. When performing analyses in the urine matrix, no alteration in the ion mobility resolving power was observed and the measured collision cross section (CCS) values varied by less than 1.0%.

CONCLUSIONS

The trapped ion mobility spectrometry-TOF mass spectrometer enabled the separation of the metabolite isomers with very small differences in CCS values (ΔCCS% = 2%). It is shown to be an effective tool for the rapid characterization of isomers in complex matrices.

Comprehensive profiling and identification of bioactive components from methanolic leaves extract of Juniperus deppeana and its in vitro antidiabetic activity

Juniperus plant species are rich sources of bioactive secondary metabolites and are traditionally used for the treatment of several illnesses, including those related to hyperglycemia and diabetes. The major bioactive compounds identified in certain species of this genus are terpenes and phenolics. Juniperus deppeana Steud. is mainly used as a wood resource and its chemical composition has been partially established. Our goal was to perform a comprehensive profiling of a methanolic extract of leaves of J. deppeana and determine its potential as a source of α-amylase and α-glucosidase inhibitors. Terpene and phenolic compounds were putatively identified based on their accurate mass spectrometric data. Regarding terpenes, we found mainly diterpenes, specifically dehydroabietic acid-like, hinokiol-like, agathic acid-like, and dihydroxyabietatrienoic acid-like compounds. Isopimaric acid was also identified and its identity was confirmed by coelution with an authentic standard via comparing retention time, mass spectrum, and collisional cross section values. For phenolic compounds, we identified mainly compounds with a chemical structure similar to the biflavonoids amentoflavone and bilobetin. Besides, the methanolic extract of J. deppeana leaves show inhibition of α-amylase (IC50 = 85.11 ± 11.91 μg mL−1) and α-glucosidase (IC50 = 32.50 ± 3.40 μg mL−1) enzymes, demonstrating a potential alternative for the search of antidiabetic natural products.

Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry

Low molecular weight metabolites are essential for defining the molecular phenotypes of cells. However, spatial metabolomics tools often lack the sensitivity, specify, and spatial resolution to provide comprehensive descriptions of these species in tissue. MALDI imaging mass spectrometry (IMS) of low molecular weight ions is particularly challenging as MALDI matrix clusters are often nominally isobaric with multiple metabolite ions, requiring high resolving power instrumentation or derivatization to circumvent this issue. An alternative to this is to perform ion mobility separation before ion detection, enabling the visualization of metabolites without the interference of matrix ions. Additional difficulties surrounding low weight metabolite visualization include high resolution imaging, while maintaining sufficient ion numbers for broad and representative analysis of the tissue chemical complement. Here, we use MALDI timsTOF IMS to image low molecular weight metabolites at higher spatial resolution than most metabolite MALDI IMS experiments (20 μm) while maintaining broad coverage within the human kidney. We demonstrate that trapped ion mobility spectrometry (TIMS) can resolve matrix peaks from metabolite signal and separate both isobaric and isomeric metabolites with different distributions within the kidney. The added ion mobility data dimension dramatically increased the peak capacity for spatial metabolomics experiments. Through this improved sensitivity, we have found >40 low molecular weight metabolites in human kidney tissue, such as argininic acid, acetylcarnitine, and choline that localize to the cortex, medulla, and renal pelvis, respectively. Future work will involve further exploring metabolomic profiles of human kidneys as a function of age, sex, and race.

Evaluation of ion mobility in capillary electrophoresis coupled to mass spectrometry for the identification in metabolomics

Currently, feature annotation remains one of the main challenges in untargeted metabolomics. In this context, the information provided by high-resolution mass spectrometry (HRMS) in addition to accurate mass can improve the quality of metabolite annotation, and MS/MS fragmentation patterns are widely used. Accurate mass and a separation index, such as retention time or effective mobility (μ_eff ), in chromatographic and electrophoretic approaches, respectively, must be used for unequivocal metabolite identification. The possibility of measuring collision cross-section (CCS) values by using ion mobility (IM) is becoming increasingly popular in metabolomic studies thanks to the new generation of IM mass spectrometers. Based on their similar separation mechanisms involving electric field and the size of the compounds, the complementarity of ^DT CCS_N2 and μ_eff needs to be evaluated. In this study, a comparison of ^DT CCS_N2 and μ_eff was achieved in the context of feature identification ability in untargeted metabolomics by capillary zone electrophoresis (CZE) coupled with HRMS. This study confirms the high correlation of ^DT CCS_N2 with the mass of the studied metabolites as well as the orthogonality between accurate mass and μ_eff , making this combination particularly interesting for the identification of several endogenous metabolites. The use of IM-MS remains of great interest for facilitating the annotation of neutral metabolites present in the electroosmotic flow (EOF) that are poorly or not separated by CZE.

Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation

INTRODUCTION

Metabolomics has become a crucial part of systems biology; however, data analysis is still often undertaken in a reductionist way focusing on changes in individual metabolites. Whilst such approaches indeed provide relevant insights into the metabolic phenotype of an organism, the intricate nature of metabolic relationships may be better explored when considering the whole system.

AREAS COVERED

This review highlights multiple network strategies that can be applied for metabolomics data analysis from different perspectives including: association networks based on quantitative information, mass spectra similarity networks to assist metabolite annotation and biochemical networks for systematic data interpretation. We also highlight some relevant insights into metabolic organization obtained through the exploration of such approaches.

EXPERT OPINION

Network based analysis is an established method that allows the identification of non-intuitive metabolic relationships as well as the identification of unknown compounds in mass spectrometry. Additionally, the representation of data from metabolomics within the context of metabolic networks is intuitive and allows for the use of statistical analysis that can better summarize relevant metabolic changes from a systematic perspective.

Metabolic Phenotyping Using UPLC–MS and Rapid Microbore UPLC–IM–MS: Determination of the Effect of Different Dietary Regimes on the Urinary Metabolome of the Rat

A rapid reversed-phase gradient method employing a 50 mm × 1 mm i.d., C18 microbore column, combined with ion mobility and high-resolution mass spectrometry, was applied to the metabolic phenotyping of urine samples obtained from rats receiving different diets. This method was directly compared to a “conventional” method employing a 150 × 2.1 mm i.d. column packed with the same C18 bonded phase using the same samples. Multivariate statistical analysis of the resulting data showed similar class discrimination for both microbore and conventional methods, despite the detection of fewer mass/retention time features by the former. Multivariate statistical analysis highlighted a number of ions that represented diet-specific markers in the samples. Several of these were then identified using the combination of mass, ion-mobility-derived collision cross section and retention time including N-acetylglutamate, urocanic acid, and xanthurenic acid. Kynurenic acid was tentatively identified based on mass and ion mobility data.

Identification of the molecular mechanism and diagnostic biomarkers in the thoracic ossification of the ligamentum flavum using metabolomics and transcriptomics

Background

To establish a metabolite fingerprint of ossification of the thoracic ligamentum flavum (OTLF) patients using liquid chromatography-mass spectrometry (LC-MS) in combination with transcriptomic data and explore the potential molecular mechanism of pathogenesis.

Results

The study cohort was composed of 25 patients with OTLF and 23 healthy volunteers as a control group. Thirty-seven metabolites were identified out by UPLC-MS including uric acid and hypoxanthine. Nine metabolites, including uric acid and hypoxanthine, were found with a Variable Importance in Projection (VIP) score over 1 (p < 0.05). Pathway enrichment indicated that purine metabolism pathways and the other four metabolism pathways were enriched. Transcriptomic data revealed that purine metabolism have a substantial change in gene expression of OTLF and that xanthine dehydrogenase (XDH) is the key regulatory factor. Receiver operating characteristic (ROC) analysis indicated that 17 metabolites, including uric acid, were found with an AUC value of over 0.7.

Conclusion

Uric acid might be the potential biomarker for OTLF and play an important role within the detailed pathway. XDH could affect purine metabolism by suppressing the expression of hypoxanthine and xanthine leading to low serum levels of uric acid in OTLF, which could be a focal point in developing new therapeutic methods for OTLF.

Analytical techniques for metabolomic studies: a review

Metabolomics is the comprehensive study of small-molecule metabolites. Obtaining a wide coverage of the metabolome is challenging because of the broad range of physicochemical properties of the small molecules. To study the compounds of interest spectroscopic (NMR), spectrometric (MS) and separation techniques (LC, GC, supercritical fluid chromatography, CE) are used. The choice for a given technique is influenced by the sample matrix, the concentration and properties of the metabolites, and the amount of sample. This review discusses the most commonly used analytical techniques for metabolomic studies, including their advantages, drawbacks and some applications.

A Novel Ion Pseudo-trapping Phenomenon within Traveling Wave Ion Guides

The widespread use of traveling wave ion mobility (TWIM) technology in fields such as omics and structural biology motivates efforts to deepen our understanding of ion transport within such devices. Here, we describe a new advancement in TWIM theory, where pseudo-trapping within TW ion guides is characterized in detail. During pseudo-trapping, ions with different mobilities can travel with the same mean velocity, leaving others within the same TWIM experiment to separate as normal. Furthermore, pseudo-trapping limits typical band broadening experienced by ions during TWIM, manifesting as peaks with apparently improved IM resolving power, but all ions that undergo pseudo trapping are unable to separate by IM. SIMION simulations show that ions become locked into a repeated pattern of motion with respect to the TW reference frame during pseudo-trapping. We developed a simplified model capable of reproducing TW pseudo-trapping and reproducing trends observed in experimental data. Our model and simulations suggest that pseudo-trapping occurs only during experiments performed under static TWIM conditions, to an extent that depends on the detailed shape of the traveling wave. We show that pseudo-trapping alters the ion transit times and can adversely affect calibrated CCS measurements. Finally, we provide recommendations for avoiding unintentional pseudo-trapping in TWIM in order to obtain optimal separations and CCS determinations.

Interlaboratory and Interplatform Study of Steroids Collision Cross Section by Traveling Wave Ion Mobility Spectrometry

Collision cross section (CCS) databases based on single-laboratory measurements must be cross-validated to extend their use in peak annotation. This work addresses the validation of the first comprehensive ^TWCCS_N2 database for steroids. First, its long-term robustness was evaluated (i.e., a year and a half after database generation; Synapt G2-S instrument; bias within ±1.0% for 157 ions, 95.7% of the total ions). It was further cross-validated by three external laboratories, including two different TWIMS platforms (i.e., Synapt G2-Si and two Vion IMS QToF; bias within the threshold of ±2.0% for 98.8, 79.9, and 94.0% of the total ions detected by each instrument, respectively). Finally, a cross-laboratory ^TWCCS_N2 database was built for 87 steroids (142 ions). The cross-laboratory database consists of average ^TWCCS_N2 values obtained by the four TWIMS instruments in triplicate measurements. In general, lower deviations were observed between ^TWCCS_N2 measurements and reference values when the cross-laboratory database was applied as a reference instead of the single-laboratory database. Relative standard deviations below 1.5% were observed for interlaboratory measurements (<1.0% for 85.2% of ions) and bias between average values and ^TWCCS_N2 measurements was within the range of ±1.5% for 96.8% of all cases. In the context of this interlaboratory study, this threshold was also suitable for ^TWCCS_N2 measurements of steroid metabolites in calf urine. Greater deviations were observed for steroid sulfates in complex urine samples of adult bovines, showing a slight matrix effect. The implementation of a scoring system for the application of the CCS descriptor in peak annotation is also discussed.

Rapid Characterization of Per- and Polyfluoroalkyl Substances (PFAS) by Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)

Per- and polyfluoroalkyl substances (PFAS) are an ensemble of persistent organic pollutants of global interest because of their associations with adverse health outcomes. Currently, environmental PFAS pollution is prolific as a result of the widespread manufacturing of these compounds and their chemical persistence. In this work, we demonstrate the advantages of adding ion mobility spectrometry (IMS) separation to existing LC-MS workflows for PFAS analysis. Using a commercially available drift tube IMS-MS, we characterized PFAS species and isomeric content in both analytical standards and environmental water samples. Molecular trendlines based on intrinsic mass and structural relationships were also explored for individual PFAS subclasses (e.g. PFSA, PFCA, etc.). Results from rapid IMS-MS analyses provided a link between mass and collision cross sections (CCS) for specific PFAS families and are linked to compositional differences in molecular structure. In addition, CCS values provide additional confidence of annotating prioritized features in untargeted screening studies for potential environmental pollutants. Results from this study show that the IMS separation provides novel information to support traditional LC-MS PFAS analyses and will greatly benefit the evaluation of unknown pollutants in future environmental studies.

Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules

Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.

Single-Cell Metabolomics by Mass Spectrometry

Single-cell level metabolomics gives a snapshot of small molecules, intermediates, and products of cellular metabolism within a biological system. These small molecules, typically less than 1 kDa in molecular weight, often provide the basis of biochemical heterogeneity within cells. The molecular differences between cells with a cell type are often attributed to random stochastic biochemical processes, cell cycle stages, environmental stress, and diseased states. In this chapter, current limitations and challenges in single-cell analysis by mass spectrometry will be discussed alongside the prospects of single-cell metabolomics in systems biology. A few selected example of the recent development in mass spectrometry tools to unravel single-cell metabolomics will be described as well.