Recent advances in biological separations using trapped ion mobility spectrometry – mass spectrometry

High-resolution ion mobility separations coupled to mass spectrometry: What's next?

Herein, I provide a personal perspective on high-resolution multipass ion mobility spectrometry-mass spectrometry (IMS-MS), with a specific emphasis on cyclic (cIMS) and structures for lossless ion manipulations (SLIM IMS)-based separations. My overarching goal for this perspective was to detail what I believe will be the key important areas in which IMS-MS will help shape the bioanalytical community and especially omics-based research.

Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry-mass spectrometry

Trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1-6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.

Identification and quantification of bipyridyl dicarboxylic acid isomers by ion mobility spectrometry

The identification of positional isomers is of interest because different isomers have different chemical or biological functions and applications. The analysis of positional isomers is sometimes challenging since they have similar chemical structures and properties. For example, the analysis of mass cannot identify different positional isomers because they have identical mass-to-charge ratios and show a single mass peak in mass spectrometry. In this study, an efficient and simple qualitative and quantitative analytical method for differentiating 2,2'-bipyridine-3,3'-dicarboxylic acid (3,3'-BDA), 2,2'-bipyridine-4,4'-dicarboxylic acid (4,4'-BDA), and 2,2'-bipyridine-5,5'-dicarboxylic acid (5,5'-BDA) was developed by using ion mobility spectrometry (IMS). The results revealed that the three BDA isomers formed non-covalent complexes with cyclodextrins (CDs) and Mg2+ ions in the gas phase: [β-CD+3,3'/4,4'/5,5'-BDA+Mg]2+ and [γ-CD+3,3'/4,4'/5,5'-BDA+Mg]2+, which were distinguished by measuring the mobility of the complexes because of their spatial conformational differences. The peak-to-peak resolution (Rp-p) values of the three isomers of [γ-CD+3,3'/4,4'/5,5'-BDA+Mg]2+ reached 2.983 and 2.892, respectively. The conformations of the ternary complexes simulated by the theoretical calculations revealed the different interactions and shapes of the stereoisomers, and the predicted results agreed with the experimental results. Simultaneously, further studies on the collisional dissociation of the ternary complexes revealed that the dissociation energies of the different complex ions varied were different owing to the diverse different conformations. Finally, the relative quantitative analysis of the different isomers in mixed samples was performed and satisfactory linearity results (R2 > 0.99) were obtained. Thus, an effective analytical method was proposed for the identification and quantification of BDA isomers without chemical derivatization, offering a promising approach for the identification of similar derivatives or positional isomers that could be applied in various fields including chemicals and pharmaceuticals.

Ultra-Fast Ion Mobility Spectrometer for High-Throughput Chromatography

Fast chromatography systems especially developed for high sample throughput applications require sensitive detectors with a high repetition rate. These high throughput techniques, including various chip-based microfluidic designs, often benefit from detectors providing subsequent separation in another dimension, such as mass spectrometry or ion mobility spectrometry (IMS), giving additional information about the analytes or monitoring reaction kinetics. However, subsequent separation is required at a high repetition rate. Here, we therefore present an ultra-fast drift tube IMS operating at ambient pressure. Short drift times while maintaining high resolving power are reached by several key instrumental design features: short length of the drift tube, resistor network of the drift tube, tristate ion shutter, and improved data acquisition electronics. With these design improvements, even slow ions with a reduced mobility of just 0.94 cm2/(V s) have a drift time below 1.6 ms. Such short drift times allow for a significantly increased repetition rate of 600 Hz compared with previously reported values. To further reduce drift times and thus increase the repetition rate, helium can be used as the drift gas, which allows repetition rates of up to 2 kHz. Finally, these significant improvements enable IMS to be used as a detector following ultra-fast separation including chip-based chromatographic systems or droplet microfluidic applications requiring high repetition rates.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

Revolutions in Lipid Isomer Resolution: Application of Ultrahigh-Resolution Ion Mobility to Reveal Lipid Diversity

Many families of lipid isomers remain unresolved by contemporary liquid chromatography-mass spectrometry approaches, leading to a significant underestimation of the structural diversity within the lipidome. While ion mobility coupled to mass spectrometry has provided an additional dimension of lipid isomer resolution, some isomers require a resolving power beyond the capabilities of conventional platforms. Here, we present the application of high-resolution traveling-wave ion mobility for the separation of lipid isomers that differ in (i) the location of a single carbon-carbon double bond, (ii) the stereochemistry of the double bond (cis or trans), or, for glycerolipids, (iii) the relative substitution of acyl chains on the glycerol backbone (sn-position). Collisional activation following mobility separation allowed identification of the carbon-carbon double-bond position and sn-position, enabling confident interpretation of variations in mobility peak abundance. To demonstrate the applicability of this method, double-bond and sn-position isomers of an abundant phosphatidylcholine composition were resolved in extracts from a prostate cancer cell line and identified by comparison to pure isomer reference standards, revealing the presence of up to six isomers. These findings suggest that ultrahigh-resolution ion mobility has broad potential for isomer-resolved lipidomics and is attractive to consider for future integration with other modes of ion activation, thereby bringing together advanced orthogonal separations and structure elucidation to provide a more complete picture of the lipidome.

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

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

Coupling Isotopic Shifts with Collision Cross-Section Measurements for Carbohydrate Characterization in High-Resolution Ion Mobility Separations

Herein, we introduce a two-dimensional strategy to better characterize carbohydrate isomers. In a single experiment, we can derive cyclic ion mobility-mass spectrometry (cIMS-MS)-based collision cross-section (CCS) values in conjunction with measuring isotopic shifts through the relative arrival times of light and heavy isotopologues. These isotopic shifts were introduced by permethylating carbohydrates with either light, CH3, or heavy, CD3, labels at every available hydroxyl group to generate a light/heavy pair of isotopologues for every individual species analyzed. We observed that our calculated CCS values, which were exclusively measured for the light isotopologues, were orthogonal to our measured isotopic shifts (i.e., relative arrival time values between heavy and light permethylated isotopologues). Our permethylation-induced isotopic shifts scaled well with increasing molecular weight, up to ∼m/z 1300, expanding the analysis of isotopic shifts to molecules 3-4 times as large as those previously studied. Our presented use of coupling CCS values with the measurement of isotopic shifts in a single cIMS-MS experiment is a proof-of-concept demonstration that our two-dimensional approach can improve the characterization of challenging isomeric carbohydrates. We envision that our presented 2D approach will have broad utility for varying molecular classes as well as being amenable to many forms of derivatization.

Exploiting ion-mobility mass spectrometry for unraveling proteome complexity

Ion mobility spectrometry-mass spectrometry (IMS-MS) is experiencing rapid growth in proteomic studies, driven by its enhancements in dynamic range and throughput, increasing the quantitation precision, and the depth of proteome coverage. The core principle of ion mobility spectrometry is to separate ions in an inert gas under the influence of an electric field based on differences in drift time. This minireview provides an introduction to IMS operation modes and a description of advantages and limitations is presented. Moreover, the principles of trapped IMS-MS (TIMS-MS), including parallel accumulation-serial fragmentation are discussed. Finally, emerging applications linked to TIMS focusing on sample throughput (in clinical proteomics) and sensitivity (single-cell proteomics) are reviewed, and the possibilities of intact protein analysis are discussed.

Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review

Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptide sequencing using tandem mass spectrometry (MS/MS) has become the main method for determining amino acid sequences of novel and unknown peptides. Advanced algorithms allow the amino acid sequence information to be accurately obtained from MS/MS spectra in short time. In this review, algorithms from exhaustive search to the state-of-art machine learning and neural network for high-throughput and automated de-novo sequencing are introduced and compared. Impacts of datasets on algorithm performance are highlighted. The current limitations and promising direction of de-novo peptide sequencing are also discussed in this review.

Using Hadamard Transform Multiplexed IR Spectroscopy Together with a Segmented Ion Trap for the Identification of Mobility-Selected Isomers

The high isomeric complexity of glycans makes them particularly difficult to analyze. While ultra-high-resolution ion mobility spectrometry (IMS) can offer rapid baseline separation of many glycan isomers, their unambiguous identification remains a challenging task. One approach to solving this problem is to identify mobility-separated isomers by measuring their highly resolved cryogenic vibrational spectra. To be able to apply this approach to complex mixtures at high throughput, we have recently developed a Hadamard transform multiplexed spectroscopic technique that allows measuring vibrational spectra of all species separated in both IMS and mass spectrometry dimensions in a single laser scan. In the current work, we further develop the multiplexing technique using ion traps incorporated directly into the IMS device based on structures for lossless ion manipulations (SLIM). We also show that multiplexed spectroscopy using perfect sequence matrices can outperform standard multiplexing using Simplex matrices. Lastly, we show that we can increase the measurement speed and throughput further by running multiple multiplexing schemes using several SLIM ion traps in combination with simultaneous spectroscopic measurements in the segmented cryogenic ion trap.

Enhancing the Depth of Analyses with Next-Generation Ion Mobility Experiments

Recent developments in ion mobility (IM) technology have expanded the capability to separate and characterize gas-phase ions of biomolecules, especially when paired with mass spectrometry. This next generation of IM technology has been ushered in by creative innovation focused on both instrument architectures and how electric fields are applied. In this review, we focus on the application of high-resolution and multidimensional IM to biomolecular analyses, encompassing the fields of glycomics, lipidomics, peptidomics, and proteomics. We highlight selected research that demonstrates the application of the new IM toolkit to challenging biomolecular systems. Through our review of recently published literature, we outline the current strengths of respective technologies and perspectives for future applications.

Integration of Trapped Ion Mobility Spectrometry and Ultraviolet Photodissociation in a Quadrupolar Ion Trap Mass Spectrometer

There is a growing demand for lower-cost, benchtop analytical instruments with complementary separation capabilities for the screening and characterization of biological samples. In this study, we report on the custom integration of trapped ion mobility spectrometry and ultraviolet photodissociation capabilities in a commercial Paul quadrupolar ion trap multistage mass spectrometer (TIMS-QIT-MSn UVPD platform). A gated TIMS operation allowed for the accumulation of ion mobility separated ion in the QIT, followed by a mass analysis (MS1 scan) or m/z isolation, followed by selected collision induced dissociation (CID) or ultraviolet photodissociation (UVPD) and a mass analysis (MS2 scan). The analytical potential of this platform for the analysis of complex and labile biological samples is illustrated for the case of positional isomers with varying PTM location of the histone H4 tryptic peptide 4-17 singly and doubly acetylated and the histone H3.1 tail (1-50) singly trimethylated. For all cases, a baseline ion mobility precursor molecular ion preseparation was obtained. The tandem CID and UVPD MS2 allowed for effective sequence confirmation as well as the identification of reporter fragment ions associated with the PTM location; a higher sequence coverage was obtained using UVPD when compared to CID. Different from previous IMS-MS implementation, the novel TIMS-QIT-MSn UVPD platform offers a lower-cost alternative for the structural characterization of biological molecules that can be widely disseminated in clinical laboratories.

How to Improve the Resolving Power of Compact Electrospray Ionization Ion Mobility Spectrometers

Every drift tube ion mobility spectrometer (IMS) has an optimum drift voltage to reach maximum resolving power. This optimum depends, among other things, on the temporal and spatial width of the injected ion packet and the pressure within the IMS. A reduction of the spatial width of the injected ion packet leads to improved resolving power, higher peak amplitudes when operating the IMS at optimum resolving power, and thus a better signal-to-noise ratio despite the reduced number of injected ions. Hereby, the performance of electrospray ionization (ESI)-IMS can be considerably improved. By setting the ion shutter opening time to just 5 μs and slightly increasing the pressure, a high resolving power R_P > 150 can be achieved with a given drift length of just 75 mm. At such high resolving power, even a mixture of the herbicides isoproturon and chlortoluron having similar ion mobility can be well separated despite short drift length.

Anticancer Drug Doxorubicin Spontaneously Reacts with GTP and dGTP

Here, we reported a spontaneous reaction between anticancer drug doxorubicin and GTP or dGTP. Incubation of doxorubicin with GTP or dGTP at 37 °C or above yields a covalent product: the doxorubicin-GTP or -dGTP conjugate where a covalent bond is formed between the C14 position of doxorubicin and the 2-amino group of guanine. Density functional theory calculations show the feasibility of this spontaneous reaction. Fluorescence imaging studies demonstrate that the doxorubicin-GTP and -dGTP conjugates cannot enter nuclei although they rapidly accumulate in human SK-OV-3 and NCI/ADR-RES cells. Consequently, the doxorubicin-GTP and -dGTP conjugates are less cytotoxic than doxorubicin. We also demonstrate that doxorubicin binds to ATP, GTP, and other nucleotides with a dissociation constant (Kd) in the sub-millimolar range. Since human cells contain millimolar levels of ATP and GTP, these results suggest that doxorubicin may target ATP and GTP, energy molecules that support essential processes in living organisms.

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

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

Integrating the potential of ion mobility spectrometry-mass spectrometry in the separation and structural characterisation of lipid isomers

It is increasingly evident that a more detailed molecular structure analysis of isomeric lipids is critical to better understand their roles in biological processes. The occurrence of isomeric interference complicates conventional tandem mass spectrometry (MS/MS)-based determination, necessitating the development of more specialised methodologies to separate lipid isomers. The present review examines and discusses recent lipidomic studies based on ion mobility spectrometry combined with mass spectrometry (IMS-MS). Selected examples of the separation and elucidation of structural and stereoisomers of lipids are described based on their ion mobility behaviour. These include fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. Recent approaches for specific applications to improve isomeric lipid structural information using direct infusion, coupling imaging, or liquid chromatographic separation workflows prior to IMS-MS are also discussed, including: 1) strategies to improve ion mobility shifts; 2) advanced tandem MS methods based on activation of lipid ions with electrons or photons, or gas-phase ion-molecule reactions; and 3) the use of chemical derivatisation techniques for lipid characterisation.

Isomer and Conformer-Specific Mass Distribution-Based Isotopic Shifts in High-Resolution Cyclic Ion Mobility Separations

Herein, we present the use of mass distribution-based isotopic shifts in high-resolution cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based separations to characterize various isomeric species as well as conformers. Specifically, by using the observed relative arrival time values for the isotopologues found in the isotopic envelope after long pathlength cIMS-MS separations, we were able to distinguish dibromoaniline, dichloroaniline, and quaternary ammonium salt isomers, as well as a pair of 25-hydroxyvitamin D3 conformers based on their respective mass distribution-based shifts. Our observed shifts were highly reproducible and broadly applied to the isotopologues of various atoms (i.e., Cl, Br, and C). Additionally, through a control experiment, we determined that such shifts are indeed pathlength-independent, thus demonstrating that our presented methodology could be readily extended to other high-resolution IMS-MS platforms. These results are the first characterization of conformers using mass distribution-based IMS-MS shifts, as well as the first use of a commercial cIMS-MS platform to characterize isomers via their mass distribution-based shifts. We anticipate that our methodology will have broad applicability for biological analytes and that mass distribution-based shifts could potentially act as an added dimension of analysis in existing IMS-MS workflows in omics-based research. Specifically, we envision that the development of a database of these mass distribution-based shifts could, for example, enable the identification of unknown metabolites in complex matrices.

Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry-Mass Spectrometry

The mammalian high mobility group protein AT-hook 2 (HMGA2) is an intrinsically disordered DNA-binding protein expressed during embryogenesis. In the present work, the conformational and binding dynamics of HMGA2 and HMGA2 in complex with a 22-nt (DNA22) and a 50-nt (DNA50) AT-rich DNA hairpin were investigated using trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) under native starting solvent conditions (e.g., 100 mM aqueous NH4Ac) and collision-induced unfolding/dissociation (CIU/CID) as well as solution fluorescence anisotropy to assess the role of the DNA ligand when binding to the HMGA2 protein. CIU-TIMS-CID-MS/MS experiments showed a significant reduction of the conformational space and charge-state distribution accompanied by an energy stability increase of the native HMGA2 upon DNA binding. Fluorescence anisotropy experiments and CIU-TIMS-CID-MS/MS demonstrated for the first time that HMGA2 binds with high affinity to the minor groove of AT-rich DNA oligomers and with lower affinity to the major groove of AT-rich DNA oligomers (minor groove occupied by a minor groove binder Hoechst 33258). The HMGA2·DNA22 complex (18.2 kDa) 1:1 and 1:2 stoichiometry suggests that two of the AT-hook sites are accessible for DNA binding, while the other AT-hook site is probably coordinated by the C-terminal motif peptide (CTMP). The HMGA2 transition from disordered to ordered upon DNA binding is driven by the interaction of the three basic AT-hook residues with the minor and/or major grooves of AT-rich DNA oligomers.

Separation and Collision Cross Section Measurements of Protein Complexes Afforded by a Modular Drift Tube Coupled to an Orbitrap Mass Spectrometer

New developments in analytical technologies and biophysical methods have advanced the characterization of increasingly complex biomolecular assemblies using native mass spectrometry (MS). Ion mobility methods, in particular, have enabled a new dimension of structural information and analysis of proteins, allowing separation of conformations and providing size and shape insights based on collision cross sections (CCSs). Based on the concepts of absorption-mode Fourier transform (aFT) multiplexing ion mobility spectrometry (IMS), here, a modular drift tube design proves capable of separating native-like proteins up to 148 kDa with resolution up to 45. Coupled with high-resolution Orbitrap MS, binding of small ligands and cofactors can be resolved in the mass domain and correlated to changes in structural heterogeneity observed in the ion-neutral CCS distributions. We also demonstrate the ability to rapidly determine accurate CCSs for proteins with 1-min aFT-IMS-MS sweeps without the need for calibrants or correction factors.

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

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

Tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS): a promising analytical method for investigating heterogenous samples

Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.

Approaches to Heterogeneity in Native Mass Spectrometry

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

Coupling Stable Isotope Labeling and Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight-Tandem Mass Spectrometry for De Novo Mosquito Ovarian Lipid Studies

There is a need to better understand lipid metabolism during mosquito ovarian development. Lipids are the major source of energy supporting ovarian follicles development in mosquitoes. In this paper, we describe the complementary use of stable isotope labeling (SIL) and high-resolution mass spectrometry-based tools for the investigation of de novo triglycerides (TG) and diglycerides (DG) during the ovarian previtellogenic (PVG) stage (4-6 days posteclosion) of female adult Aedes aegypti. Liquid chromatography coupled to high-resolution trapped ion mobility spectrometry-parallel accumulation sequential fragmentation-time-of-flight tandem mass spectrometry (LC-TIMS-PASEF-TOF MS/MS) allowed the separation and quantification of nonlabeled and 2H/13C-labeled TG and DG species. Three SIL strategies were evaluated (H2O/2H2O with 50:50 and 95:5 mixtures, 13C-sucrose, and 13C-glucose). Results showed wide applicability with no signs of lipid ovarian impairment by SIL induced toxicity. The analytical workflow based on LC-TIMS-TOF MS/MS provided high confidence and high reproducibility for lipid DG and TG identification and SIL incorporation based on their separation by retention time (RT), collision cross section (CCS), and accurate m/z. In addition, the SIL fatty acid chain incorporation was evaluated using PASEF MS/MS. The 2H/13C incorporation into the mosquito diet provided information on how TG lipids are consumed, stored, and recycled during the PVG stage of ovarian development.

The chirality determination of amino acids by forming complexes with cyclodextrins and metal ions using ion mobility spectrometry, and a DFT calculation

Chiral recognition is of highly interest in the areas of chemistry, pharmaceuticals, and bioscience. An effective strategy of enantiomeric determination of amino acids (AAs) was developed in this work. All 19 natural AAs enantiomers can be easily distinguished by ion mobility-mass spectrometry of the non-covalent complexes of AAs with cyclodextrins (α-CD, β-CD and γ-CD) and Mg²⁺ without any chemical derivatization. Differences of the mobilities between the enantiomers' complexes is from 0.006 to 0.058 V s/cm². In addition, the complex of [β-CD + Phe + Mg]²⁺ was selected as an example to study the relative quantification by measuring L/D-Phe at different molar ratio of 10:1 to 1:10 in the μM range, resulting in a good linearity (R² > 0.99) and high sensitivity at 2 μM. A DFT calculation was also performed to illustrate the detailed molecular structure of the complexes of CDs, Mg²⁺ and D- or L-Phe. Both experiment and theoretical calculation showed that Mg²⁺ plays an important role in host/guest interactions, which changed the molecular conformations by non-covalent interaction between Mg²⁺ and CDs, and resulted in the different collision cross-sections of the complex ions of CDs, Mg²⁺ and D- or L-AAs in the gas phase. This effective and convenient strategy could potentially be utilized in scientific research and industry for routine enantiomeric determination of natural AAs, peptides and some other small chiral biomolecules such as non-natural AAs and carboxylic acid-containing drugs.

Experimental Measurements of Relative Mobility Shifts Resulting from Isotopic Substitutions with High-Resolution Cyclic Ion Mobility Separations

Herein, we report on the experimental measurements for estimated relative mobility shifts caused by changes in mass distribution from isotopic substitutions in isotopologues and isotopomers with high-resolution cyclic ion mobility separations. By utilizing unlabeled and fully labeled isotopologues with the same isotopic substitutions (i.e., ²H or ¹³C), we created a highly precise mobility scale for each set analyzed to determine the magnitude of such mass distribution shifts and thus calculate estimated deviations from expected, theoretical reduced mass contributions. We observed relative mobility shifts in various isotopologues (e.g., hexadecyltrimethylammonium, sucrose, and palmitic acid species) that deviated from reduced mass theory, according to the Mason-Schamp relationship, ranging in estimated magnitude from ∼0.007% up to ∼0.1% in relative mobility. More interestingly, it was found that two deuterated palmitic acid isotopomers also differed by ∼0.03% from one another in their respective relative mobility shifts. Our results are the first report of isotopologue and isotopomer separations on a commercially available cyclic ion mobility spectrometry-mass spectrometry platform. We envision that our presented mobility scale methodology will have broad applicability in studying the effect of mass distribution changes from isotopic substitutions in other biomolecules and help pave the way for the improvement of ion mobility theory and collision cross section calculators.

Systematic Optimization of Ambient Ionization Ion Mobility Mass Spectrometry for Rapid Separation of Isomers

Current methods typically used for metabolite screening and disease diagnosis often require extensive sample preparation, which increases analysis time and associated costs. While ambient ionization techniques enable the analysis of various samples in complex matrices with little or no sample preparation in a short time (typically within a minute), their reduced selectivity, even when coupled with high-resolution mass spectrometers, limits their application in certain fields. In this study, we have optimized the coupling of paper spray (PS) and leaf spray (LS) ambient ionization techniques with a commercially available ion mobility mass spectrometer (IM-MS) and demonstrated the separation of geometric and constitutional isomers. Ambient ionization techniques allow simultaneous introduction and ionization of samples, while background noise and matrix interference from paper and leaf substrates are filtered out by IM separation, resulting in high sensitivity and selectivity of the PS-IM-MS and LS-IM-MS workflows. In addition, we introduced a novel approach to perform single-field collision cross section (CCS) measurements, which resulted in CCS values that differ by 0.15% and 0.25% from traditional stepped-field and single-field methods, respectively. In addition, we used advanced computational tools to confidently identify analyte structures by comparing CCS values from experimental IM measurements and theoretical calculations. These results suggest that the coupling of ambient ionization methods with ion mobility techniques enables rapid, sensitive, and highly selective analysis that can be used in different fields, such as agrochemical screening and disease diagnostics.

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

INTRODUCTION

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

AREAS COVERED

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

EXPERT OPINION

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

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

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

Substrate Sequence Controls Regioselectivity of Lanthionine Formation by ProcM

Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). The (methyl)lanthionine cross-links characteristic to lanthipeptides are essential for their stability and bioactivities. In most bacteria, lanthipeptides are maturated from single precursor peptides encoded in the corresponding biosynthetic gene clusters. However, cyanobacteria engage in combinatorial biosynthesis and encode as many as 80 substrate peptides with highly diverse sequences that are modified by a single lanthionine synthetase into lanthipeptides of different lengths and ring patterns. It is puzzling how a single enzyme could exert control over the cyclization processes of such a wide range of substrates. Here, we used a library of ProcA3.3 precursor peptide variants and show that it is not the enzyme ProcM but rather its substrate sequences that determine the regioselectivity of lanthionine formation. We also demonstrate the utility of trapped ion mobility spectrometry-tandem mass spectrometry (TIMS-MS/MS) as a fast and convenient method to efficiently separate lanthipeptide constitutional isomers, particularly in cases where the isomers cannot be resolved by conventional liquid chromatography. Our data allowed identification of factors that are important for the cyclization outcome, but also showed that there are no easily identifiable predictive rules for all sequences. Our findings provide a platform for future deep learning approaches to allow such prediction of ring patterns of products of combinatorial biosynthesis.

Investigating the Structure of α/β Carbohydrate Linkage Isomers as a Function of Group I Metal Adduction and Degree of Polymerization as Revealed by Cyclic Ion Mobility Separations

In high-resolution ion mobility spectrometry-mass spectrometry (IMS-MS)-based separations individual, pure, oligosaccharide species often produce multiple IMS peaks presumably from their α/β anomers, cation attachment site conformations, and/or other energetically favorable structures. Herein, the use of high-resolution traveling wave-based cyclic IMS-MS to systematically investigate the origin of these multiple peaks by analyzing α1,4- and β1,4-linked d-glucose homopolymers as a function of their group I metal adducts is presented. Across varying degrees of polymerization, and for certain metal adducts, at least two major IMS peaks with relative areas that matched the ∼40:60 ratio for the α/β anomers of a reducing-end d-glucose as previously calculated by NMR were observed. To further validate that these were indeed the α/β anomers, rather than other substructures, the reduced versions of several maltooligosaccharides were analyzed and all produced a single IMS peak. This result enabled the discovery of a mobility fingerprint trend: the β anomer was always higher mobility than the α anomer for the cellooligosaccharides, while the α anomer was always higher mobility than the β anomer for the maltooligosaccharides. For maltohexaose, a spurious, high mobility, fourth peak was present. This was hypothesized to potentially be from a highly compacted conformation. To investigate this, α-cyclodextrin, a cyclic oligosaccharide, produced similar arrival times as the high mobility maltohexaose peak. It is anticipated that these findings will aid in the data deconvolution of IMS-MS-based glycomics workflows and enable the improved characterization of biologically relevant carbohydrates.

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.

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry

Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.

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

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

Toward Sequencing the Human Milk Glycome: High-Resolution Cyclic Ion Mobility Separations of Core Human Milk Oligosaccharide Building Blocks

Human milk oligosaccharides (HMOs) are an unconjugated class of glycans that have been implicated for their role in promoting the healthy development of the brain-gut axes of infants. Production of HMOs is ever-changing and specifically tailored for each infant in response to various biological factors (e.g., cognitive development, diseases, or allergies). While every HMO consists of up to only five monosaccharides, their structures can be composed of many possible glycosidic linkage positions and corresponding α/β anomericities, linear or branched chains, and potential fucosylation/sialylation modifications, thus leading to a tremendous degree of isomeric heterogeneity. With limited availability of authentic standards for every putative HMO structure (estimated to be >200 total), new analytical methods are needed for their accurate characterization. Complete sequencing of the human milk glycome would enable a better understanding of their infant-specific biological roles and potentially lead to their widespread incorporation into infant formula. Herein, we explore the use of our high-resolution cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based platform for the separation of core disaccharide and trisaccharide isomer building blocks as a first step toward the sequencing of larger HMOs. By utilizing the flexible capabilities of the cIMS array, separation pathlengths were extended up to 40 m, thus enabling the resolution of all seven sets of sialylated, fucosylated galactosyllactose and lactosamine HMO building block isomers. Additionally, we assessed the utility of pre-/post-cIMS tandem mass spectrometry (MS/MS) and tandem cIMS (cIMS/cIMS) for the characterization of HMOs based on their diagnostic fragmentation patterns and mobility fingerprints. We anticipate that our presented cIMS-MS-based methodology will enable the better characterization of larger, unknown HMOs when incorporated into an overall workflow that also includes online liquid chromatography and enzymatic hydrolyses.

Proteoform Differentiation using Tandem Trapped Ion Mobility, Electron Capture Dissociation, and ToF Mass Spectrometry

Comprehensive characterization of post-translationally modified histone proteoforms is challenging due to their high isobaric and isomeric content. Trapped ion mobility spectrometry (TIMS), implemented on a quadrupole/time-of-flight (Q-ToF) mass spectrometer, has shown great promise in discriminating isomeric complete histone tails. The absence of electron activated dissociation (ExD) in the current platform prevents the comprehensive characterization of unknown histone proteoforms. In the present work, we report for the first time the use of an electromagnetostatic (EMS) cell devised for nonergodic dissociation based on electron capture dissociation (ECD), implemented within a nESI-TIMS-Q-ToF mass spectrometer for the characterization of acetylated (AcK18 and AcK27) and trimethylated (TriMetK4, TriMetK9 and TriMetK27) complete histone tails. The integration of the EMS cell in a TIMS-q-TOF MS permitted fast mobility-selected top-down ECD fragmentation with near 10% efficiency overall. The potential of this coupling was illustrated using isobaric (AcK18/TriMetK4) and isomeric (AcK18/AcK27 and TriMetK4/TriMetK9) binary H3 histone tail mixtures, and the H3.1 TriMetK27 histone tail structural diversity (e.g., three IMS bands at z = 7+). The binary isobaric and isomeric mixtures can be separated in the mobility domain with R_IMS > 100 and the nonergodic ECD fragmentation permitted the PTM localization (sequence coverage of ∼86%). Differences in the ECD patterns per mobility band of the z = 7+ H3 TriMetK27 molecular ions suggested that the charge location is responsible for the structural differences observed in the mobility domain. This coupling further enhances the structural toolbox with fast, high resolution mobility separations in tandem with nonergodic fragmentation for effective proteoform differentiation.

Structural Heterogeneity of Human Histone H2A.1

Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.

Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses

Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.

Synergistically Bifunctional Paramagnetic Separation Enables Efficient Isolation of Urine Extracellular Vesicles and Downstream Phosphoproteomic Analysis

Extracellular vesicles (EVs) have emerged as important carriers for intercellular communication and biological sources for diagnosis and therapeutics. Low efficiency in EV isolation from biofluids, however, severely restricts their downstream characterization and analysis. Here, we introduced a novel strategy for EV isolation from urine for prostate cancer diagnosis using bifunctionalized magnetic beads through high affinity Ti(IV) ions and the insertion of a phospholipid derivative, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine, into the EV membrane synergistically. We demonstrated its efficient isolation of EVs from urine samples with low contamination, high recovery (>80%), and short separation time (within 1 h), resulting in the identification of 36,262 unique EV peptides corresponding to 3302 unique proteins and 3233 unique phosphopeptides representing 1098 unique phosphoproteins using only 100 μL and 5 mL urine samples, respectively. Coupled with trapped ion mobility spectrometry and parallel accumulation-serial fragmentation for phosphosite-specific resolution, quantitative phosphoproteomics of urine samples from prostate cancer patients and healthy individuals revealed 121 upregulated phosphoproteins in cancer patients in contrast to the healthy group. These particular advantages indicate that the novel bifunctional material enables sensitive EV phosphoproteomic analysis for noninvasive biomarker screening and early cancer diagnosis.

Mapping chemotherapeutic drug distribution in cancer cell spheroids using 2D-TOF-SIMS and LESA-TIMS-MS

Three-dimensional (3D) cancer cell cultures grown in the form of spheroids are effective models for the study of in vivo-like processes simulating cancer tumor pharmacological dynamics and morphology. In this study, we show the advantages of Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) combined with in situ Liquid Extraction Surface Analysis coupled to trapped Ion Mobility Spectrometry Mass Spectrometry (LESA-TIMS-TOF MS) for high spatial resolution mapping and quantitation of ABT-737, a chemotherapeutic drug, at the level of single human colon carcinoma cell spheroids (HCT 116 MCS). 2D-TOF-SIMS studies of consecutive sections (∼16 μm thick slices) showed that ABT-737 is homogenously distributed in the outer layers of the HCT 116 MCS. Complementary in situ LESA-TIMS-TOF MS/MS measurements confirmed the presence of the ABT-737 drug in the MCS slides by the observation of the molecular ion [M + H]+m/z and mobility, and the charateristic fragmentation pattern. LESA-TIMS-TOF MS allowed a quantitative assessment of the ABT-737 drug of the control MCS slice spiked with ABT-737 standard over the 0.4-4.1 ng range and MCS treated starting at 10 μM for 24 h. These experiments showcase an effective protocol for unambigous characterization and 3D mapping of chemotherapeutic drug distribution at the single MCS level.

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.

Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11

In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH (e.g., pH 3.1-6.1) and concentration (e.g., 1-50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged (e.g., [M]+, [M - 2H + NH4]+, [M - H + Na]+ and [M - H + K]+) and doubly charged (e.g., [M + H]2+, [M - H + NH4]2+, [M + Na]2+ and [M + K]2+) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity (e.g., number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges (e.g., NH4 +, Na+ and K+ vs. H+). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge (i.e., a CE50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H]3+, [2M - H + NH4]3+, [2M + Na]3+ and [2M + K]3+, respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species.

Application of the UHPLC-DIA-HRMS Method for Determination of Cheese Peptides

Until now, cheese peptidomics approaches have been criticised for their lower throughput. Namely, analytical gradients that are most commonly used for mass spectrometric detection are usually over 60 or even 120 min. We developed a cheese peptide mapping method using nano ultra-high-performance chromatography data-independent acquisition high-resolution mass spectrometry (nanoUHPLC-DIA-HRMS) with a chromatographic gradient of 40 min. The 40 min gradient did not show any sign of compromise in milk protein coverage compared to 60 and 120 min methods, providing the next step towards achieving higher-throughput analysis. Top 150 most abundant peptides passing selection criteria across all samples were cross-referenced with work from other publications and a good correlation between the results was found. To achieve even faster sample turnaround enhanced DIA methods should be considered for future peptidomics applications.

Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry

The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).

Can IM-MS Collision Cross Sections of Biomolecules Be Rationalized Using Collision Cross-Section Trends of Polydisperse Synthetic Homopolymers?

In the past, we developed a method inferring physicochemical properties from ion mobility mass spectrometry (IM-MS) data from polydisperse synthetic homopolymers. We extend here the method to biomolecules that are generally monodisperse. Similarities in the IM-MS behavior were illustrated on proteins and peptides. This allows one to identify ionic species for which intramolecular interactions lead to specific structures.