Fundamentals of trapped ion mobility spectrometry

Development of a Structure for Lossless Ion Manipulations (SLIM) High Charge Capacity Array of Traps

Enhancing the sensitivity of low-abundance ions in a complex mixture without sacrificing measurement throughput is highly desirable. This work demonstrates a way to greatly improve the sensitivity of ion mobility (IM)-selected ions by accumulating them in an array of high-capacity ion traps located inside a novel structures for lossless ion manipulations ion mobility spectrometer (SLIM-IMS) module. The array of ion traps used in this work consisted of seven independently controllable traps. Each trap was 386 mm long and possessed a charge capacity of ∼4.5 × 108 charges, with a linear range extending to ∼2.5 × 108 charges. Each ion trap could be used to extract a peak (or ions over a mobility range) from an ion mobility separation based on arrival time. Ions could be stored without losses for long times (>100 s) and then released all at once or one trap at a time. It was possible to accumulate large ion populations by extracting and storing ions over repeated IM separations. Enrichment of up to seven individual ion distributions could be performed using the seven independently controllable ion traps. Additionally, the ion trapping process effectively compressed ion populations into narrow peaks, which provides a greatly improved basis for subsequent ion manipulations. The array of high charge capacity ion traps provides a flexible addition to SLIM and a powerful tool for IMS-MS applications requiring high sensitivity.

Combining trapped ion mobility spectrometry with liquid chromatography and tandem mass spectrometry for analysis of isomeric PDE-5 inhibitor analogs

The detection and identification of phosphodiesterase type 5 enzyme (PDE-5) inhibitors in dietary supplements poses an analytical challenge due to the large number of analogs and isomers currently available and the continued introduction of novel analogs. The use of trapped ion mobility spectrometry (TIMS) in conjunction with liquid chromatography (LC) and electrospray ionization tandem mass spectrometry (MS/MS) was explored for the analysis of two groups of isomeric PDE-5 inhibitor analogs using a 5-minute method. Of the eight compounds studied, six were resolved by a combination of LC and TIMS; the two remaining isomers were distinguished by one or more unique product ions in the MS/MS spectrum. The results revealed that separation by LC corresponded to differences in substitution on the piperazine moiety of the PDE-5 inhibitors, while separation by TIMS corresponded to the position of a nitrogen atom in the fused ring region of the molecules. Samples prepared by spiking mixtures of varying amounts of the Group 2 isomers into a representative dietary supplement matrix were analyzed and concentrations determined from the mobility-adjusted extracted ion chromatograms exhibited relative standard deviations of 6.0 % or less for 17 of 20 measurements and recoveries between 80 % and 120 % for all measurements. Quantitative measurements from a short LC gradient were possible due to the reduced chemical background associated with the TIMS separation of co-eluting matrix compounds, which enabled acquisition of rapid and qualitatively relevant broadband collision induced dissociation spectra that didn't require precursor ion isolation; the reduced chemical background permits non-targeted detection of novel analogs and eliminates the need for a separate method for quantitative measurement.

Understanding of protomers/deprotomers by combining mass spectrometry and computation

Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

Rapid discrimination of enantiomers by ion mobility mass spectrometry and chemical theoretical calculation: Chiral mandelic acid and its derivatives

Because R/S-mandelic acids (MA) and their derivatives are critical starting materials or intermediates in the synthesis of chiral drugs, their chirality discrimination is important. In this study, R/S-MA and its derivatives, including R/S-2-phenylpropionic acid (2-PPA), R/S-methoxyphenylaceticacid (MPA), and R/S-2-hydroxy-4-phenylbutyric acid (HPBA), were accurate simultaneous mobility-discriminated by forming diastereomer complexes for the first time, which were obtained by simply mixing with cyclodextrins (α, β, γ-CD) and transition-metal ions (Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺). The mass spectra revealed non-covalent diastereomer complexes formed by CD, enantiomers, and metal ions, and ion-mobility spectrometry (IMS) was performed for 109 pairs of complexes. Significant chiral discrimination was observed in the formed diastereomeric complexes, and their separation peak-to-peak resolution (R_p-p) for the enantiomers depended on the transition metal ion type. In most cases, the R_p-p value gradually increases with CD size, with quaternary complexes having the largest R_p-p value. The greatest chiral distinctions of 2-PPA, MA, MPA, and HPBA were obtained by the diastereomeric complex ions of [(2-PPA)(α)₂+Zn²⁺-H]⁺, [(MA)(α)₂+Zn²⁺-H]⁺, [(MPA)₂(β)+Co²⁺-H]⁺, and [(HPBA)(α)₂+Fe²⁺-H]⁺, with R_p-p values of 1.35, 1.57, 1.70, and 0.71, respectively. Furthermore, the favorable conformation and collisional cross section (CCS) value of the different [CD + R/S-MA + Cu-H]⁺ complexes were measured using chemical theoretical calculations to detail their intermolecular interaction, revealing that [α-CD + R/S-MA + Cu-H]⁺ has two favored gas complexes, and the CCS calculated were consistent with the TIMS observed. In addition, R² > 0.99 was obtained for the relative quantification of the chiral enantiomers. Overall, the proposed method provides a promising strategy for distinguishing the enantiomers of MA and their derivatives, with the advantages of simplicity, speed, and accuracy, without the need for complex chemical derivatization or chromatographic separation.

ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics

Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the high levels of data reduction that occur between raw data and machine learning-ready data. Since predictive proteomics is an emerging field, when predicting peptide behavior in LC-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility. For this reason we introduce ProteomicsML, an online resource for proteomics-based data sets and tutorials across most of the currently explored physicochemical peptide properties. This community-driven resource makes it simple to access data in easy-to-process formats, and contains easy-to-follow tutorials that allow new users to interact with even the most advanced algorithms in the field. ProteomicsML provides data sets that are useful for comparing state-of-the-art machine learning algorithms, as well as providing introductory material for teachers and newcomers to the field alike. The platform is freely available at https://www.proteomicsml.org/, and we welcome the entire proteomics community to contribute to the project at https://github.com/ProteomicsML/ProteomicsML.

Differentiation of Isomeric, Nonseparable Carbohydrates Using Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry

Carbohydrates play important roles in biological processes, but their identification remains a significant analytical problem. While mass spectrometry has increasingly enabled the elucidation of carbohydrates, current approaches are limited in their abilities to differentiate isomeric carbohydrates when these are not separated prior to tandem-mass spectrometry analysis. This analytical challenge takes on increased relevance because of the pervasive presence of isomeric carbohydrates in biological systems. Here, we demonstrate that TIMS2-MS2 workflows enabled by tandem-trapped ion mobility spectrometry-mass spectrometry (tTIMS/MS) provide a general approach to differentiate isomeric, nonseparated carbohydrates. Our analysis shows that (1) cross sections measured by TIMS are sufficiently precise and robust for ion identification; (2) fragment ion cross sections from TIMS2 analysis can be analytically exploited to identify carbohydrate precursors even if the precursor ions are not separated by TIMS; (3) low-abundant fragment ions can be exploited to identify carbohydrate precursors even if the precursor ions are not separated by IMS. (4) MS2 analysis of fragment ions produced by TIMS2 can be used to validate and/or further characterize carbohydrate structures. Taken together, our analysis underlines the opportunities that tandem-ion mobility spectrometry/MS methods offer for the characterization of mixtures of isomeric carbohydrates.

MALDI TIMS IMS of Disialoganglioside Isomers─GD1a and GD1b in Murine Brain Tissue

Gangliosides are acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or more sialic acid residue(s) and are highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility spectrometry with MALDI IMS allows for the analysis of isomeric lipid structures in situ. Here, we demonstrate the gas-phase separation and identification of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in multiple samples, including a standard mixture of both isomers, a biological extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) isomers were determined in rat hippocampus and spinal cord tissue sections, demonstrating the ability to structurally characterize and spatially map gangliosides based on both the carbohydrate chain and ceramide moieties.

Top-Down Ion Mobility Separations of Isomeric Proteoforms

Continuing advances in proteomics highlight the ubiquity and biological importance of proteoforms─proteins with varied sequence, splicing, or distribution of post-translational modifications (PTMs). The preeminent example is histones, where the PTM pattern encodes the combinatorial language controlling the DNA transcription central to life. While the proteoforms with distinct PTM compositions are distinguishable by mass, the isomers with permuted PTMs commonly coexisting in cells generally require separation before mass-spectrometric (MS) analyses. That was accomplished on the bottom-up and middle-down levels using chromatography or ion mobility spectrometry (IMS), but proteolytic digestion obliterates the crucial PTM connectivity information. Here, we demonstrate baseline IMS resolution of intact isomeric proteoforms, specifically the acetylated H4 histones (11.3 kDa). The proteoforms with a single acetyl moiety on five alternative lysine residues (K5, K8, K12, K16, K20) known for distinct functionalities in vivo were constructed by two-step native chemical ligation and separated using trapped IMS at the resolving power up to 350 on the Bruker TIMS/ToF platform. Full resolution for several pairs was confirmed using binary mixtures and by unique fragments in tandem MS employing collision-induced dissociation. This novel capability for top-down proteoform characterization is poised to open major new avenues in proteomics and epigenetics.

Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters

Coupling drift tube ion mobility (IM) to Fourier transform mass spectrometry (FT-MS) affords the opportunity for gas-phase separation of ions based on size and conformation with high-resolution mass analysis. However, combining IM and FT-MS is challenging because ions exit the drift tube on a much faster time scale than the rate of mass analysis. Fourier transform (FT) and Hadamard transform multiplexing methods have been implemented to overcome the duty-cycle mismatch, offering new avenues for obtaining high-resolution, high-mass-accuracy analysis of mobility-selected ions. The gating methods used to integrate the drift tube with the FT mass analyzer discriminate against the transmission of large, low-mobility ions owing to the well-known gate depletion effect. Tristate gating strategies have been shown to increase ion transmission for drift tube IM-FT-MS systems through implementation of dual ion gating, controlling the quantity and timing of ions through the drift tube to reduce losses of slow-moving ions. Here we present an optimized set of multiplexing parameters for tristate gating ion mobility of several proteins on an Orbitrap mass spectrometer and further report parameters for increased ion transmission and mobility resolution as well as decreased experimental times from 15 min down to 30 s. On average, peak intensities in the arrival time distributions (ATDs) for ubiquitin increased 2.1× on average, while those of myoglobin increased by 1.5× with a resolving power increase on average of 11%.

Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations

BACKGROUND

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

AIM OF REVIEW

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

KEY SCIENTIFIC CONCEPTS OF REVIEW

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

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.

Top-"Double-Down" Mass Spectrometry of Histone H4 Proteoforms: Tandem Ultraviolet-Photon and Mobility/Mass-Selected Electron Capture Dissociations

Post-translational modifications (PTMs) on intact histones play a major role in regulating chromatin dynamics and influence biological processes such as DNA transcription, replication, and repair. The nature and position of each histone PTM is crucial to decipher how this information is translated into biological response. In the present work, the potential of a novel tandem top-"double-down" approach─ultraviolet photodissociation followed by mobility and mass-selected electron capture dissociation and mass spectrometry (UVPD-TIMS-q-ECD-ToF MS/MS)─is illustrated for the characterization of HeLa derived intact histone H4 proteoforms. The comparison between q-ECD-ToF MS/MS spectra and traditional Fourier-transform-ion cyclotron resonance-ECD MS/MS spectra of a H4 standard showed a similar sequence coverage (∼75%) with significant faster data acquisition in the ToF MS/MS platform (∼3 vs ∼15 min). Multiple mass shifts (e.g., 14 and 42 Da) were observed for the HeLa derived H4 proteoforms for which the top-down UVPD and ECD fragmentation analysis were consistent in detecting the presence of acetylated PTMs at the N-terminus and Lys5, Lys8, Lys12, and Lys16 residues, as well as methylated, dimethylated, and trimethylated PTMs at the Lys20 residue with a high sequence coverage (∼90%). The presented top-down results are in good agreement with bottom-up TIMS ToF MS/MS experiments and allowed for additional description of PTMs at the N-terminus. The integration of a 213 nm UV laser in the present platform allowed for UVPD events prior to the ion mobility-mass precursor separation for collision-induced dissociation (CID)/ECD-ToF MS. Selected c305+ UVPD fragments, from different H4 proteoforms (e.g., Ac + Me2, 2Ac + Me2 and 3Ac + Me2), exhibited multiple IMS bands for which similar CID/ECD fragmentation patterns per IMS band pointed toward the presence of conformers, adopting the same PTM distribution, with a clear assignment of the PTM localization for each of the c305+ UVPD fragment H4 proteoforms. These results were consistent with the biological "zip" model, where acetylation proceeds in the Lys16 to Lys5 direction. This novel platform further enhances the structural toolbox with alternative fragmentation mechanisms (UVPD, CID, and ECD) in tandem with fast, high-resolution mobility separations and shows great promise for global proteoform analysis.

State-of-the-art glycosaminoglycan characterization

Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.

Comparability of Steroid Collision Cross Sections Using Three Different IM-HRMS Technologies: An Interplatform Study

Steroids play key roles in various biological processes and are characterized by many isomeric variants, which makes their unambiguous identification challenging. Ion mobility-mass spectrometry (IM-MS) has been proposed as a suitable platform for this application, particularly using collision cross section (CCS) databases obtained from different commercial IM-MS instruments. CCS is seen as an ideal additional identification parameter for steroids as long-term repeatability and interlaboratory reproducibility of this measurand are excellent and matrix effects are negligible. While excellent results were demonstrated for individual IM-MS technologies, a systematic comparison of CCS derived from all major commercial IM-MS technologies has not been performed. To address this gap, a comprehensive interlaboratory comparison of 142 CCS values derived from drift tube (DTIM-MS), traveling wave (TWIM-MS), and trapped ion mobility (TIM-MS) platforms using a set of 87 steroids was undertaken. Besides delivering three instrument-specific CCS databases, systematic comparisons revealed excellent interlaboratory performance for 95% of the ions with CCS biases within ±1% for TIM-MS and within ±2% for TWIM-MS with respect to DTIM-MS values. However, a small fraction of ions (<1.5%) showed larger biases of up to 7% indicating that differences in the ion conformation sampled on different instrument types need to be further investigated. Systematic differences between CCS derived from different IM-MS analyzers and implications on the applicability for nontargeted analysis are critically discussed. To the best of our knowledge, this is the most comprehensive interlaboratory study comparing CCS from three different IM-MS technologies for analysis of steroids and small molecules in general.

Simulation study of inverse diffusion counterbalance method for super-resolution ion mobility spectrometry

Ion mobility spectrometer (IMS) is a powerful chemical composition analysis tool working at atmospheric pressure that can be used to separate complex samples and study molecular structures. Resolution is a key parameter for evaluating the performance of IMS. However, for the pulsed sampling technique used by drift tube IMS, there is an upper limit to the resolution due to the diffusion between ions and the drift gas. In this work, an inverse diffusion counterbalance method is proposed to break the resolution limit. The method is inspired by the stimulated emission depletion (STED). In optical microscopy systems, STED is used to break the optical diffraction limit by a ring of depleted light to counteract diffraction effects of the excited light. We modified this strategy and applied it to an IMS system for counteracting the diffusion effect of the pulsed ion packet. The method can increase the resolution up to 1.55 times through theoretical analysis, and the improvement is verified by simulations. The simulation results find that the initial width of the ion packet has an influence on the effectiveness of the method, and the narrower the initial width, the better the effect. The proposed inverse counterbalance strategy may also be applied to other spectral analysis instruments to break the resolution limit.

Quantitation of Enantiomeric Excess in an Achiral Environment Using Trapped Ion Mobility Mass Spectrometry

We present a novel, straightforward method to determine the enantiomeric excess (ee) of tryptophan (Trp) and N-tert-butyloxycarbonyl-O-benzylserine (BBS) solutions without chiral additives. For this, lithium carbonate, sodium carbonate, or silver acetate was added to solutions of Trp or BBS. Singly negatively charged dimer and trimer clusters were then formed by electrospray ionization and analyzed using trapped ion mobility spectrometry (TIMS) and time-of-flight mass spectrometry. When a solution contains both enantiomers, homo- and heterochiral clusters are generated which can be separated in the TIMS-tunnel based on their different mobilities using a nitrogen buffer gas. The ratio of homochiral to heterochiral clusters shows a binomial distribution and can be calibrated with solutions of known ee to yield ee measurements of samples with better than 1% accuracy. Samples can be prepared rapidly, and measurements are completed in less than 5 min. Current instrumental limitations restrict this method to rigid molecules with large functional groups adjacent to the chiral centers. Nevertheless, we expect this method to be applicable to many pharmaceuticals and provide the example of 1-methyltryptophan to demonstrate this.

Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics

Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.

Where have all the ions gone, long time passing? Tandem quadrupole mass spectrometers with atmospheric pressure ionization sensitivity gains since the mid-1970s. A perspective

The gains in sensitivity since 1975 for quadrupole mass spectrometers equipped with atmospheric pressure ionization (API), and in particular triple quadrupole mass spectrometers (QqQs) since 1981, have been driven by the needs of the environmental, biomedical, agricultural, and other scientific research, industrial, regulatory, legal, and sporting communities to continually achieve lower limits of quantitation and identification. QqQs have realized a one-million-fold improvement in sensitivity attempting to address these needs over the past two score years. It is the purpose of this article to describe how that came about, not through an exhaustive review of the literature, but rather by describing what general approaches were used across the industry to improve sensitivity and provide some examples to illustrate its evolution. The majority of the gains came from the ion source and its interface to the vacuum system. "Sampling efficiency" is a measurement of the losses in this area so will be a focus of this review. The discovery of the phenomenon of collisional focusing was key to improving sampling efficiency because it enabled designs that increased the ion-containing gas loads from the ion source, using staged differential pumping backed by increasingly larger pumps, and prevented the scattering losses of ions in the resulting gas expansion inside vacuum. Likewise, systems with smaller pumps and lower ion-containing gas loads could be designed with size and cost reduction in mind while maintaining reasonable sampling efficiencies. As a consequence, advancements in the designs of both larger and smaller turbomolecular vacuum pumps were accelerated by pump manufacturers to accommodate the explosive growth in the use of API-QqQ and API-ion trap mass spectrometers that occurred in the 1990s and continued into the new millennium. Sampling efficiency was further improved by increasing the ion yield from electrospray by increasing the rate of droplet desolvation. An estimate of the practical limit to further sensitivity improvements beyond what has been achieved to date is provided to shed light on what to expect in the future. Lastly, the implications and unforeseen consequences of the sensitivity gains are considered with a particular focus on how they have enabled a dramatic increase in daily sample throughput on triple quadrupole and other types of mass spectrometers.

Trapped Ion Mobility Spectrometry, Ultraviolet Photodissociation, and Time-of-Flight Mass Spectrometry for Gas-Phase Peptide Isobars/Isomers/Conformers Discrimination

Trapped ion mobility spectrometry (TIMS) when coupled with mass spectrometry (MS) offers great advantages for the separation of isobaric, isomeric, and/or conformeric species. In the present work, we report the advantages of coupling TIMS with a low-cost, ultraviolet photodissociation (UVPD) linear ion trap operated at few mbars prior to time-of-flight (ToF) MS analysis for the effective characterization of isobaric, isomeric, and/or conformeric species based on mobility-selected fragmentation patterns. These three traditional challenges to MS-based separations are illustrated for the case of biologically relevant model systems: H3.1 histone tail PTM isobars (K4Me3/K18Ac), lanthipeptide regioisomers (overlapping/nonoverlapping ring patterns), and a model peptide conformer (angiotensin I). The sequential nature of the TIMS operation allows for effective synchronization with the ToF MS scans, in addition to parallel operation between the TIMS and the UVPD trap. Inspection of the mobility-selected UVPD MS spectra showed that for all three cases considered, unique fragmentation patterns (fingerprints) were observed per mobility band. Different from other IMS-UVPD implementations, the higher resolution of the TIMS device allowed for high mobility resolving power (R > 100) and effective mobility separation. The mobility selected UVPD MS provided high sequence coverage (>85%) with a fragmentation efficiency up to ∼40%.

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.

Indirect Enantioseparations: Recent Advances in Chiral Metabolomics for Biomedical Research

Chiral metabolomics is starting to become a well-defined research field, powered by the recent advances in separation techniques. This review aimed to cover the most relevant advances in indirect enantioseparations of endogenous metabolites that were published over the last 10 years, including improvements and development of new chiral derivatizing agents, along with advances in separation methodologies. Moreover, special emphasis is put on exciting advances in separation techniques combined with mass spectrometry, such as chiral discrimination by ion-mobility mass spectrometry together with untargeted strategies for profiling of chiral metabolites in complex matrices. These advances signify a leap in chiral metabolomics technologies that will surely offer a solid base to better understand the specific roles of enantiomeric metabolites in systems biology.

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

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

Exploiting Self-Association to Evaluate Enantiomeric Composition by Cyclic Ion Mobility–Mass Spectrometry

The characterization of enantiomers is an important analytical challenge in the chemical and life sciences. Thorough evaluation of the purity of chiral molecules is particularly required in the pharmaceutical industry where safety concerns are paramount. Assessment of the enantiomeric composition is still challenging and time-consuming, meaning that alternative approaches are required. In this study, we exploit the formation of dimers as diastereomeric pairs of enantiomers to affect separation by high resolution cyclic ion mobility–mass spectrometry. Using the example of (R/S)-thalidomide, we show that even though this is not an enantiomer separation, we can determine which enantiomer is in excess and obtain quantitative information on the enantiomer composition without the need for a chiral modifier. Further examples of the approach are presented, including d/l-tryptophan and (R/S)-propanolol, and demonstrate the need for mobility resolving power in excess of 400 (CCS/ΔCCS).

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.

Supercritical Fluid Chromatography Coupled with Drift Time Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry as a Tool for Lipid Characterization of HepG2 Cells

Lipidomic studies are often conducted using shotgun mass spectrometry (MS) or reversed-phase liquid chromatography coupled with MS (LC–MS). However, chromatographic separation offers several advantages such as an additional identification parameter (retention time), lower ion suppression, and separation of isobaric species. In contrast, quantification is more difficult because ion suppression is not the same over the whole analysis, and as a consequence more standards are needed to compensate for this. Supercritical fluid chromatography (SFC) offers orthogonal separation compared to reversed-phase LC. While the separation of lipids in reversed-phase LC is mainly based on the length of the carbon chain and the number of double bonds, lipids in SFC are mainly separated according to their lipid classes, which simplifies quantification with standards. In this study, SFC coupled with drift time ion mobility quadrupole time-of-flight mass spectrometry (DTIMS-QTOF-MS)was used to characterize the HepG2 lipidome.

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.

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

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

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper's transparent peer review process is included in the supplemental information.

In Silico Collision Cross Section Calculations to Aid Metabolite Annotation

The interpretation of ion mobility coupled to mass spectrometry (IM-MS) data to predict unknown structures is challenging and depends on accurate theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low or atmospheric pressure drift chamber. The sensitivity and reliability of computational prediction of CCS values depend on accurately modeling the molecular state over accessible conformations. In this work, we developed an efficient CCS computational workflow using a machine learning model in conjunction with standard DFT methods and CCS calculations. Furthermore, we have performed Traveling Wave IM-MS (TWIMS) experiments to validate the extant experimental values and assess uncertainties in experimentally measured CCS values. The developed workflow yielded accurate structural predictions and provides unique insights into the likely preferred conformation analyzed using IM-MS experiments. The complete workflow makes the computation of CCS values tractable for a large number of conformationally flexible metabolites with complex molecular structures.

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.

Ion Mobility Studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes

Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the past decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently convert alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here, we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry, and quantum-chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas-phase structures of [PQQH₂]^-, [PQQH₂+H₂O]^-, [PQQH₂+MeOH]^-, [PQQ-15c5+H]⁺, and [PQQ-15c5+Ln+NO₃]²⁺ (Ln = La to Lu, except Pm). In the latter case, a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in the future such investigations will help to guide the design and understanding of lanthanide-based biomimetic complexes optimized for catalytic function.

Anionic Stacks of Alkali-Interlinked Yttrium and Dysprosium Bicyclooctatetraenes in Isolation

Electrospray ionization of THF solutions of preformed [K(18-c-6)][M(COT)₂] (M = Dy(III), Y(III); COT = C₈H₈^2-,18-c-6 = C₁₂H₂₄O₆) yields the isolated species [(M(COT)₂)_n+1 + nK]^- with n = 0-3. High-resolution ion mobility spectrometry combined with density functional theory calculations performed for the n = 0-2 aggregates indicate that anionic multidecker stacks interlinked by potassium cations are formed. The alternating metal ions are aligned linearly: COT^2--M³⁺-COT^2--K⁺-COT^2--M³⁺-COT^2-. The different M³⁺ ionic radii lead to slight but resolvable changes in mobility and thus collision cross sections indicative of different overall heights of the multidecker stacks. CID measurements show that the aggregates fragment by cleavage at the K⁺ interconnections.

Separation of Isomeric Metabolites and Gangliosides with High Performance (Drift Tube) Ion Mobility–Mass Spectrometry

The study of metabolites and gangliosides is increasingly important in drug discovery (1) and immunology (2). Accurate analysis of biologically relevant isomers is important because their structure affects their molecular properties. Typically, the isomers are separated using chromatography prior to mass spectrometry (MS) analysis. However, specialized chromatographic methods that distinguish isomers frequently require a complex setup and long runs. Techniques that allow accurate results to be acquired quickly and efficiently would be beneficial.

Influence Exerted by the Solvent Effect on the Mobility Peak of 1,8-Naphthalic Anhydride in Ion Mobility Spectrometry

The collision cross-section (CCS) values of ions determined by ion mobility-mass spectrometry (IM-MS) can be used to deduce the shape and size of the ions. For each compound, as well as its isomer or tautomer, a unique arrival time peak was obtained in extracted ion mobility (EIM) spectra, which corresponded to a specific CCS value. However, the generation of solvated ions by electrospray ionization (ESI) increases the number of mobility peaks, which makes the EIM spectra difficult to interpret. In this study, solvent clusters formed by acetonitrile and methanol around 1,8-naphthalic anhydride (1,8-NA) cations ([C₁₂H₆O₃ + H]⁺_1,8-NA) were investigated using trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOF MS). The effects of infusion flow rate, nebulizer gas pressure, drying gas rate, and drying gas temperature on the formation of solvent clusters from acetonitrile and methanolic solution were systematically studied. The formation of solvent clusters was observed with infusion flow rates increased, which was manifested by the larger experimental CCS values of [C₁₂H₆O₃ + H]⁺_1,8-NA. Acetonitrile tended to form solvent clusters around ions more readily than methanol. These solvent clusters were stable enough to be detected by TIMS, but they cannot survive under ion activation conditions of mass spectrometry (MS). Increasing the nebulizer gas pressure seems to be a better way to eliminate the formation of solvent clusters in TIMS-TOF MS and give a "cleaner" EIM spectra. The current research demonstrates that more attention should be paid to the solvent effect on CCS values and their interpretation.

Detection of Mycotoxins in Highly Matrix-Loaded House-Dust Samples by QTOF-HRMS, IM-QTOF-HRMS, and TQMS: Advantages and Disadvantages

The analysis of (trace) contaminants in environmental samples represents an important tool for exposure assessment and for the evaluation of potential risks to human health. Currently, mass spectrometric detection using triple quadrupole (TQMS) systems is the established method of choice. However, screening methods using high resolution mass spectrometry (HRMS) find increasing application as they provide advantages such as enhanced selectivity. A complex composition of environmental samples is known to have enormous effects on mass analyzers. The present work therefore compares the impact of a highly matrix-loaded sample material like house-dust on the performance of mass spectrometric detection of the emerging indoor contaminant group of mycotoxins by quadrupole time-of-flight (QTOF) and TQMS after ultrahigh-performance liquid chromatographic separation. Furthermore, the role of ionization efficiencies of different ion sources in instrument sensitivity was compared using an electrospray ionization source and a newly developed heated electrospray ion source (Bruker VIP-HESI) during QTOF experiments. Finally, it was evaluated whether an additional dimension of separation enables increased sensitivity in QTOF-HRMS detection by applying mycotoxins in house-dust to an (trapped) ion mobility spectrometry instrument. The sensitivity of the QTOF detection was positively influenced by the application of the VIP-HESI ion source, and overall HRMS instruments provided enhanced selectivity resulting in simplified data evaluation compared to the TQMS. However, all performed experiments revealed strong signal suppression due to matrix components. QTOF results showed more severe effects, enabling a more sensitive detection of mycotoxins in house-dust by applying TQMS detection.

Improved Identification of Proteoforms in Top-Down Proteomics Using FAIMS with Internal CV Stepping

In top-down (TD) proteomics, prefractionation prior to mass spectrometric (MS) analysis is a crucial step for both the high confidence identification of proteoforms and increased proteome coverage. In addition to liquid-phase separations, gas-phase fractionation strategies such as field asymmetric ion mobility spectrometry (FAIMS) have been shown to be highly beneficial in TD proteomics. However, so far, only external compensation voltage (CV) stepping has been demonstrated for TD proteomics, i.e., single CVs were applied for each run. Here, we investigated the use of internal CV stepping (multiple CVs per acquisition) for single-shot TD analysis, which has huge advantages in terms of measurement time and the amount of sample required. In addition, MS parameters were optimized for the individual CVs since different CVs target certain mass ranges. For example, small proteoforms identified mainly with more negative CVs can be identified with lower resolution and number of microscans than larger proteins identified primarily via less negative CVs. We investigated the optimal combination and number of CVs for different gradient lengths and validated the optimized settings with the low-molecular-weight proteome of CaCo-2 cells obtained using a range of different sample preparation techniques. Compared to measurements without FAIMS, both the number of identified protein groups (+60-94%) and proteoforms (+46-127%) and their confidence were significantly increased, while the measurement time remained identical. In total, we identified 684 protein groups and 2675 proteoforms from CaCo-2 cells in less than 24 h using the optimized multi-CV method.

Recognition of Cis-Trans and Chiral Proline and Its Derivatives by Ion Mobility Measurement of Their Complexes with Natamycin and Metal Ion

Discrimination of isomers is an important and valuable feature in many analytical applications, and the identification of chiral isomers and cis-trans isomers is the current research focus. In this work, a simple method for direct, simultaneous recognition of d-/l-proline (P), d-/l-/cis-/trans-4-hydroxyproline (4-HP), and d-/l-/cis-/trans-N-tert-butoxycarbony (N-Boc-4-HP) was investigated by means of trapped ion mobility spectrometry-mass spectrometry (TIMS-MS). The isomers with cis-/trans-/d-/l-configuration can be directly recognized based on their mobility upon reaction with natamycin (Nat) and metal ions through noncovalent interactions. The results indicate that the recognition of the enantiomers has certain specificity, and the structural difference of the enantiomers was increased in a complex with Nat and metal ions. Herein, d-/l-P can be recognized through the ternary complexes [P + Nat + Mg - H]⁺, [P + 2Nat + Ca - H]⁺, [P + 2Nat + Mn - H]⁺, and [P + Nat + Cu - H]⁺. Similarly, c-4-HP_L, c-4-HP_D, t-4-HP_L, and t-4-HP_D can be recognized by [4-HP + Nat + Ca - H]⁺, [4-HP + 2Nat + Ca - H]⁺, and [4-HP + Nat + Cu - H]⁺, while N-Boc-c-4-HP_L, N-Boc-c-4-HP_D, N-Boc-t-4-HP_L, and N-Boc-t-4-HP_D were recognized through the enantiomer complexes [N-Boc-4-HP + Nat + Li]⁺, [N-Boc-4-HP + Nat + 2Na - H]⁺, [N-Boc-4-HP + Nat + K]⁺, [N-Boc-4-HP + Nat + Mn - H]⁺, and [N-Boc-4-HP + Nat + Ba - H]⁺. Moreover, tandem mass spectrometry (MS/MS) results indicated that different collision energies were obtained for the same fragment ions, which implied that the enantiomer complexes that contributed to their mobility separation shared identical interaction mode but had different gas-phase rigid geometries. Furthermore, the relative quantification for the enantiomers was performed, and the results were supported by a satisfactory coefficient (R² > 0.99). The developed method can provide a promising and powerful strategy for the separation of chiral proline and its d-/l-/cis-/trans derivatives, bearing the advantages of higher speed, better accuracy, high selectivity, and no need for chemical derivatization and chromatographic separation.

An overlapping peaks separation algorithm for ion mobility spectrometry based on second-order differentiation and dynamic inertia weight particle swarm optimization algorithm

RATIONALE

Ion mobility spectrometry (IMS) is a powerful analytical tool extensively applied in numerous domains. However, there still exists the phenomenon of peaks overlapping in the analysis of isomers with similar structures due to the limited resolution of IMS. In this paper, a dynamic inertia weight particle swarm optimization (DIWPSO) algorithm combined with second-order differentiation is proposed to separate the IMS overlapping peaks efficiently and precisely.

METHODS

It can identify the component number of overlapping peaks and limit those parameters (ion mobility, intensity, and full-width at half maximum of each single peak) of the peak model in a small range using second-order differentiation. Based on this, DIWPSO that has been set the best operating parameters is capable of accurately separating IMS overlapping peaks to identify the compound within a short time.

RESULTS

A comparison between the performance of DIWPSO and the improved particle swarm optimization (IPSO) found that DIWPSO with separation errors less than 2.34% overall outperforms IPSO whose maximum error is up to 5.58%. Moreover, the running time of DIWPSO is 30-80 times less than that of IPSO, and DIWPSO exhibits stronger robustness.

CONCLUSIONS

This method can automatically identify the component number of IMS overlapping peaks and resolve them with muticomponents and different overlapped degrees rapidly and accurately, which further improves the structural resolution of IMS.

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions

The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.

Collision-Induced Unfolding of Native-like Protein Ions Within a Trapped Ion Mobility Spectrometry Device

Native mass spectrometry and collision-induced unfolding (CIU) workflows continue to grow in utilization due to their ability to rapidly characterize protein conformation and stability. To perform these experiments, the instrument must be capable of collisionally activating ions prior to ion mobility spectrometry (IMS) analyses. Trapped ion mobility spectrometry (TIMS) is an ion mobility implementation that has been increasingly adopted due to its inherently high resolution and reduced instrumental footprint. In currently deployed commercial instruments, however, typical modes of collisional activation do not precede IMS analysis, and thus, the instruments are incapable of performing CIU. In this work, we expand on a recently developed method of activating protein ions within the TIMS device and explore its analytical utility toward the unfolding of native-like protein ions. We demonstrate the unfolding of native-like ions of ubiquitin, cytochrome C, β-lactoglobulin, and carbonic anhydrase. These ions undergo extensive unfolding upon collisional activation. Additionally, the improved resolution provided by the TIMS separation uncovers previously obscured unfolding complexity.

Recent technological developments for native mass spectrometry

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