Rapid and sensitive differentiation of anomers, linkage, and position isomers of disaccharides using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS)

Racetrack FAIMS for High-Resolution and High-Sensitivity Characterization of Peptide Conformers

A racetrack field asymmetric waveform ion mobility spectrometry (r-FAIMS) device, which consists of both cylindrical FAIMS (c-FAIMS) and planar FAIMS (p-FAIMS) sections with a 1 mm gap width, was developed and applied for high-resolution and high-sensitivity exploration of conformational diversity for peptides. The optimal operating conditions of r-FAIMS were systemically studied, and the performance of the fully optimized r-FAIMS was compared to a previously developed p-FAIMS in detail by using pure nitrogen as the FAIMS carrier gas. Relying on the ion focusing effect in the c-FAIMS section, the intensity of the FAIMS spectrum for doubly charged bradykinin ions acquired by using r-FAIMS is ∼8.5-fold higher than that acquired by using p-FAIMS under the same resolving power/resolution condition, implying about an order of magnitude better sensitivity of r-FAIMS. In addition, the peak separation resolution of r-FAIMS was ∼1.70-fold higher than p-FAIMS under a similar sensitivity condition for doubly charged bradykinin ions. Due to a reduced gap width of the newly designed r-FAIMS (1 mm) as compared to the previously developed p-FAIMS (1.88 mm), r-FAIMS can operate at a much higher separation field with a similar FAIMS dispersion voltage (DV) to gain significantly higher resolving power. For triply charged syntide 2 ions, the resolving power of r-FAIMS can easily exceed 120 at -3.5 kV DV by using pure nitrogen as the FAIMS carrier gas as compared to 44.2 resolving power obtained by using p-FAIMS at -4.0 kV DV. All of the experimental results have confirmed that r-FAIMS can perform structural characterization of biomolecules with both high resolution and high sensitivity.

Simulation study of a new racetrack FAIMS analyzer to achieve both high-resolution and high-sensitivity

A new racetrack field-asymmetric waveform ion mobility spectrometry (r-FAIMS) analyzer was developed in this study by combining the existing planar FAIMS (p-FAIMS) and cylindrical FAIMS (c-FAIMS). The ion inlet and outlet regions of r-FAIMS were consisted of a half of c-FAIMS, respectively, and these c-FAIMS were further connected by two p-FAIMS to form a racetrack shaped FAIMS. With such FAIMS working electrode configuration, the ions entering the r-FAIMS can be focused and separated in the first c-FAIMS section, be further separated in the p-FAIMS section with high-resolution, be focused and separated again in the final c-FAIMS section and eventually enter the mass spectrometer or other analyzers for analysis. Detailed simulation by using SIMION software with the default FAIMS user program showed that the ion focusing effect in the first c-FAIMS section ensures the ions entering the following p-FAIMS section as a compact ion packet. This effectively decreases the ion loss caused by Coulomb repulsion and thermal diffusion in p-FAIMS section as compared to the ions being introduced into the p-FAIMS gap randomly in the conventional design. As a result, the ion transmission efficiency of r-FAIMS is at least 3.3-fold higher than the single p-FAIMS under the operating conditions used in this study. The ion trajectory simulation results also showed that the resolving power of r-FAIMS is about the sum of the resolving powers for its c-FAIMS and p-FAIMS sections. The resolving power of r-FAIMS is at least 3.6-fold higher than the single c-FAIMS under the operation conditions used in this study. Therefore, the r-FAIMS can realize both high-resolution and high-sensitive ion mobility separation.

Application and integration of deep learning in FAIMS for identifying acetone concentration

In practical applications, analytical instruments are used for both qualitative and quantitative analysis. However, for high-field asymmetric-waveform ion mobility spectrometry (FAIMS), most studies to date have been focused on the qualitative analysis of substances, with limited research on quantitative analysis. Explored here is the feasibility of using deep learning in FAIMS for quantitative analysis, aided by redesigning the FAIMS upper computer. Integrating spectrum creation and deep learning analysis into the FAIMS upper computer boosts the processing and analysis of FAIMS data, laying a foundation for applying FAIMS practically. For analysis using image processing, multiple FAIMS spectral lines obtained under different conditions are converted into a three-dimensional thermodynamic map known as a FAIMS spectrum, and multiple FAIMS spectrum are preprocessed to obtain the data set of this experiment. The principles of partial-least-squares regression and the XGBoost and ResNeXt models are introduced in detail, and the data are analyzed using these models, while exploring the effects of different model parameters and determining their optimal values. The experimental results show that the pre-trained ResNeXt deep learning model performs the best on the test set, with a root mean square error of 0.86 mg/mL, indicating the potential of deep learning in realizing quantitative analysis of substances in FAIMS.

A high-performance standalone planar FAIMS system for effective detection of chemical warfare agents via TSPSO algorithm

A high-performance standalone planar field asymmetric waveform ion mobility spectrometry (p-FAIMS) system with a deconvolution algorithm (two-step particle swarm optimization algorithm, TSPSO) for overlapping peaks was developed to effectively detect chemical warfare agents (CWAs). Four CWA simulants were applied in this study to systemically evaluate the performance of the standalone p-FAIMS system. The experimental results showed that each CWA simulant in the mixture can be positively identified by carefully comparing the compensation voltage (CV) value of each peak in the FAIMS spectra for the mixture to the ones in the spectra acquired by using the same FAIMS system for the pure CWA simulant standards. The FAIMS spectrum of the CWA simulant mixture might consist of multiple overlapping peaks, which would be difficult to accurately determine the CV value for each CWA simulant peak. This problem has been effectively resolved in this study by deconvoluting the overlapping peaks via the TSPSO algorithm. As the effective peak deconvolution via TSPSO requires the degree of overlap between each FAIMS peak to be lower than a specific value, the flow rate of FAIMS carrier gas was decreased to further improve the resolution of the p-FAIMS system. After the accurate deconvolution, the resolution of original FAIMS spectrum can also be enhanced to achieve baseline separation by using TSPSO algorithm to narrow the peak width of each peak. The experimental results in this study demonstrated the possibility of using TSPSO algorithm to achieve high-resolution on a typically low-resolution standalone FAIMS. The concept in this study can potentially be applied to any low-resolution instruments to achieve high-resolution results.

Ion mobility mass spectrometry enables the discrimination of positional isomers and the detection of conformers from cyclic oligosaccharides-metals supramolecular complexes

Cyclic oligosaccharides are well known to interact with various metals, able to form supramolecular complexes with distinct sizes and shapes. However, the presence of various isomers in a sample, including positional isomers and conformers, can significantly impact molecular recognition, encapsulation ability and chemical reactivity. Therefore, it is crucial to have tools for deep samples probing and correlation establishments. The emerging ion mobility mass spectrometry (IM-MS) has the advantages to be rapid and sensitive, but is still in its infancy for the investigation of supramolecular assemblies. In the herein study, it was demonstrated that IM-MS is suitable to discriminate several isomers of cyclodextrins (CD)-metals complexes, used as cyclic oligosaccharide models. In this sense, we investigated branched 6-O-α-glucosyl- or 6-O-α-maltosyl-β-cyclodextrins (G1-β-CD and G2-β-CD) and their purely cyclic isomers: CD8 (γ-CD) and CD9 (δ-CD). The corresponding collision cross section (CCS) values were deducted for the main positive singly and doubly charged species. Experimental CCS values were matched with models obtained from molecular modelling. The high mobility resolving power and resolution enabled discrimination of positional isomers, identification of various conformers and accurate relative content estimation. These results represent a milestone in the identification of carbohydrate conformers that cannot be easily reached by other approaches.

Charge Inversion Ion/Ion Reactions Coupled to Ion Mobility/Mass Spectrometry: Oligosaccharides

Various ion mobility-based separation techniques and instruments have been recently developed to increase the operational resolution of ion mobility separations, especially of isomers and isobars. In addition to developments in instrumentation, different covalent and noncovalent derivatization techniques have helped achieve effective separations by magnifying minor differences in collision cross section. Among these methodologies is host-guest complex formation and, a new development presented herein, charge inversion ion-ion reactions coupled to ion mobility separations. We used these methods to enable formation of complexes between isomeric deprotonated oligosaccharides and alkaline earth metals (in solution) and alkaline earth metal-trisphenanthroline complexes (in vacuo), observing minor shifts in ion mobility arrival times for the charge inversion reaction products as well as unique mobility fingerprints indicative of separations of α/β anomers of disaccharides. For example, we have demonstrated separations between reducing disaccharides such as lactose and lactulose and nonreducing disaccharides. We also observed separations based on the pyranose/furanose configurations of the isomers. These results suggest the potential for ion/ion reactions to enable isomer separation of biomolecules from various compound classes using ion mobility-mass spectrometry (IM-MS).

High-field asymmetric waveform ion mobility spectrometry for xylene isomer separation assisted by helium-chemical modifiers

We propose a combined helium-chemical modifier method for a faster and more convenient separation and detection of xylene isomers. The method employs high-field asymmetric waveform ion mobility spectrometry (FAIMS) to investigate the separation and identification of three xylene isomers. A homemade hollow needle-ring ion source was used, and five chemical modifiers, represented by methanol, ethanol, acetone, ethyl acetate, and acetic acid, were doped into the xylene target analytes to observe the separation and identification of the three isomers. This was based on the fact that the addition of helium and the increase of the RF voltage could no longer improve the resolution of the field asymmetric waveform ion mobility spectrometry system. The experimental results at an RF field voltage of 15 kV cm^-1 showed that the spectral peak shifts of o-, m-, and p-xylene in a normal nitrogen environment were -0.21, -0.21, and -0.24 V, respectively. o-Xylene showed a spectral peak of -1.33 V after the addition of helium; however, the separation was not evident. The FAIMS spectrum of xylene showed multiple cluster ion peaks upon addition of the chemical modifiers on top of helium. The alcohol chemical modifiers caused three spectral peaks, with the best effect for methanol, and the characteristic ion peak positions of -7.16, -6.90, and -6.01 V for o-, m-, and p-xylene, respectively. The separation using proton-based chemical modifiers was confirmed to be stronger than that using non-proton-based chemical modifiers, and appropriate volume fractions of chemical modifiers provided a better separation of the target analytes. This study introduces a novel concept and method for the separation and identification of xylene isomers.

Evaluating the Utility of Temporal Compression in High-Resolution Traveling Wave-Based Cyclic Ion Mobility Separations

Ion mobility spectrometry coupled to mass spectrometry (IMS-MS) is slowly becoming a more integral part in omics-based workflows. With the recent technological advancements in IMS-MS instrumentation, particularly those involving traveling wave-based separations, ultralong pathlengths have become readily available in commercial platforms (e.g., Select Series Cyclic IMS from Waters Corporation and MOBIE from MOBILion). However, a tradeoff exists in such ultralong pathlength separations: increasing peak-to-peak resolution at the cost of lower signal intensities and thus poorer sensitivity of measurements. Herein, we explore the utility of temporal compression, where ions are compressed in the time domain, following high-resolution cyclic ion mobility spectrometry-mass spectrometry-based separations on a commercially available, unmodified platform. We assessed temporal compression in the context of various separations including those of reverse sequence peptide isomers, chiral noncovalent complexes, and isotopologues. From our results, we demonstrated that temporal compression improves IMS peak intensities by up to a factor of 4 while only losing ∼5 to 10% of peak-to-peak resolution. Additionally, the improvement in peak quality and signal-to-noise ratio was evident when comparing IMS-MS separations with and without a temporal compression step performed. Temporal compression can readily be implemented in existing traveling wave-based IMS-MS platforms, and our initial proof-of-concept demonstration shows its promise as a tool for improving peak shapes and peak intensities without sacrificing losses in resolution.

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.

Two-Dimensional FAIMS-IMS Characterization of Peptide Conformers with Resolution Exceeding 1000

A high-performance field asymmetric waveform ion mobility spectrometry (FAIMS)-IMS-MS platform was developed and applied to explore the conformational diversity of the singly and doubly charged bradykinin (BK + H⁺)⁺ and (BK + 2H⁺)²⁺ ions. With pure N₂ as the FAIMS carrier gas, more than ten conformers of (BK + H⁺)⁺ can be resolved using FAIMS-IMS, as compared to only four conformers resolved using either FAIMS or IMS alone. Interestingly, multiple conformers of (BK + H⁺)⁺ were found to have completely different values of FAIMS compensation voltage (CV), while their IMS drift times were essentially the same, which were also proven experimentally to not result from the structural annealing by the collisional heating in the ion funnel. The separations in the FAIMS and IMS dimensions are substantially orthogonal, and the overall resolving power of two-dimensional FAIMS-IMS separation is largely proportional to the product of the separation resolving powers of FAIMS and IMS. Using a gas mixture of N₂/He to further improve the resolving power of the FAIMS separation, the total resolving powers of the combined FAIMS and IMS separation were estimated to be about 1020 and 1400 for (BK + H⁺)⁺ and (BK + 2H⁺)²⁺ ions, respectively, which are significantly higher than the resolving power of any ion mobility-based separation techniques demonstrated so far. The combined FAIMS-IMS can thus be a much more powerful technique to explore the structural diversity of biomolecules.

Application of zero-phase digital filtering for effective denoising of field asymmetric waveform ion mobility spectrometry signal

RATIONALE

Field asymmetric waveform ion mobility spectrometry (FAIMS) has a great potential to become a portable technology for rapid detection of chemical and biological agents. However, the ion current signals, measured at the exit of the planar FAIMS directly, may contain different types of noises. The peak information in the FAIMS spectrum, such as the compensation voltage (CV) value at the maximum peak intensity (CV_P ) and the peak width at half maximum (W_h ), could not be accurately determined under the weak signal condition, which significantly limits the achievable instrument sensitivity, and there are no existing solutions to the problem.

METHODS

This study analyzed the noise type of FAIMS signal in detail, and three different signal processing algorithms, such as median filtering (MF), discrete wavelet transform (DWT), and zero-phase digital filtering (ZDF), were evaluated for their performance in denoising the FAIMS signal.

RESULTS

The results show that the standard deviation of CV_p obtained from the signal denoised using ZDF algorithm is at least 31.82% smaller as compared to using MF and DWT algorithms. The standard deviation of W_h is at least 45.45% smaller using ZDF algorithm. Moreover, only ZDF algorithm can keep the percentage error for the CV value of the denoised signal to be within 0.50 ± 0.47% of the true CV value, implying the effectiveness of ZDF algorithm in denoising while retaining the integrity of the signal.

CONCLUSIONS

The ZDF algorithm greatly reduces the analyte peak extraction error and improves the limit of detection in FAIMS measurements.

Disentangling Lipid Isomers by High-Resolution Differential Ion Mobility Spectrometry/Ozone-Induced Dissociation of Metalated Species

The preponderance and functional importance of isomeric biomolecules have become topical in biochemistry. Therefore, one must distinguish and identify all such forms across compound classes, over a wide dynamic range as minor species often have critical activities. With all the power of modern mass spectrometry for compositional assignments by accurate mass, the identical precursor and often fragment ion masses render this task a steep challenge. This is recognized in proteomics and epigenetics, where proteoforms are disentangled and characterized employing novel separations and non-ergodic dissociation mechanisms. This issue is equally pertinent to lipidomics, where the lack of isomeric depth has thwarted the deciphering of functional networks. Here we introduce a new platform, where the isomeric lipids separated by high-resolution differential ion mobility spectrometry (FAIMS) are identified using ozone-induced dissociation (OzID). Cationization by metals (here K⁺, Ag⁺, and especially Cu⁺) broadly improves the FAIMS resolution of isomers with alternative C═C double bond (DB) positions or stereochemistry, presumably via metal attaching to the DB and reshaping the ion around it. However, the OzID yield diminishes for Ag⁺ and vanishes for Cu⁺ adducts. Argentination still strikes the best compromise between efficient separation and diagnostic fragmentation for optimal FAIMS/OzID performance.

Ion Mobility Spectrometry of Superheated Macromolecules at Electric Fields up to 500 Td

Since its inception in 1980s, differential or field asymmetric waveform ion mobility spectrometry (FAIMS) has been implemented at or near ambient gas pressure. We recently developed FAIMS at 15-30 Torr with mass spectrometry and utilized it to analyze amino acids, isomeric peptides, and protein conformers. The separations broadly mirrored those at atmospheric pressure, save for larger proteins that (as predicted) exhibited dipole alignment at ambient but not low pressure. Here we reduce the pressure down to 4.7 Torr, allowing normalized electric fields up to 543 Td-double the maximum in prior FAIMS or IMS studies of polyatomic ions. Despite the collisional heating to ∼1000 °C at the waveform peaks, the proteins of size from ubiquitin to albumin survived intact. The dissociation of macromolecules in FAIMS appears governed by the average ion temperature over the waveform cycle, unlike the isomerization controlled by the peak temperature. The global separation trends in this "superhot" regime extend those at moderately low pressures, with distinct conformers and no alignment as theorized. Although the scaling of the compensation voltage with the field fell below cubic at lower fields, the resolving power increased and the resolution of different proteins or charge states substantially improved.

Separation of isomeric cereal-derived arabinoxylan-oligosaccharides by collision induced dissociation-travelling wave ion mobility spectrometry-tandem mass spectrometry (CID-TWIMS-MS/MS)

The potential of travelling wave ion mobility spectroscopy in combination with collision induced dissociation tandem mass spectrometry (CID-TWIMS-MS/MS) to separate cereal-derived isomeric arabinoxylan-oligosaccharides (A)XOS was investigated. Three trisaccharide, four tetrasaccharide, and four pentasaccharide (A)XOS isomers were analyzed by positive and negative ionization TWIMS-MS and CID-TWIMS-MS/MS. The tri- and pentasaccharide isomers were distinguishable by the ATDs of the precursor ions. The CID-TWIMS-MS/MS could separate most of the isomeric fragment ions produced from tetra- and pentasaccharide (A)XOS. Finally, the base peak mobility spectrum is introduced as a practical tool for (A)XOS fingerprinting.

Resolving Power and Collision Cross Section Measurement Accuracy of a Prototype High-Resolution Ion Mobility Platform Incorporating Structures for Lossless Ion Manipulation

A production prototype structures for lossless ion manipulation ion mobility (SLIM IM) platform interfaced to a commercial high-resolution mass spectrometer (MS) is described. The SLIM IM implements the traveling wave ion mobility technique across a ∼13m path length for high-resolution IM (HRIM) separations. The resolving power (CCS/ΔCCS) of the SLIM IM stage was benchmarked across various parameters (traveling wave speeds, amplitudes, and waveforms), and results indicated that resolving powers in excess of 200 can be accessed for a broad range of masses. For several cases, resolving powers greater than 300 were achieved, notably under wave conditions where ions transition from a nonselective "surfing" motion to a mobility-selective ion drift, that corresponded to ion speeds approximately 30-70% of the traveling wave speed. The separation capabilities were evaluated on a series of isomeric and isobaric compounds that cannot be resolved by MS alone, including reversed-sequence peptides (SDGRG and GRGDS), triglyceride double-bond positional isomers (TG 3, 6, 9 and TG 6, 9, 12), trisaccharides (melezitose, raffinose, isomaltotriose, and maltotriose), and ganglioside lipids (GD1b and GD1a). The SLIM IM platform resolved the corresponding isomeric mixtures, which were unresolvable using the standard resolution of a drift-tube instrument (∼50). In general, the SLIM IM-MS platform is capable of resolving peaks separated by as little as ∼0.6% without the need to target a specific separation window or drift time. Low CCS measurement biases <0.5% were obtained under high resolving power conditions. Importantly, all the analytes surveyed are able to access high-resolution conditions (>200), demonstrating that this instrument is well-suited for broadband HRIM separations important in global untargeted applications.

Sweet systems: technologies for glycomic analysis and their integration into systems biology

Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.

Delineation of Isomers by the 13C Shifts in Ion Mobility Spectra

Mass spectrometry (MS) and isotopes were intertwined for a century, with stable isotopes central to many MS identification and quantification protocols. In contrast, the analytical separations including ion mobility spectrometry (IMS) largely ignored isotopes, partly because of insufficient resolution. We recently delineated various halogenated aniline isomers by structurally specific splitting in FAIMS spectra. While this capability hinges on the ¹³C shifts, all preceding studies leveraged ³⁷Cl or ⁸¹Br to enhance the differentiation. However, such abundant heavy isotopes are absent from typical organic compounds. With single I isotope, iodinated organics generate similar isotopic envelopes dominated by the ¹³C atoms. Here, we distinguish the three monoiodoaniline isomers based on the shifts solely for one or two ¹³C atoms. The differentiation may be somewhat improved using multipoint peak position descriptions for more reproducible shifts. The interisomer order of shifts differs from those for chlorinated or brominated analogues, showcasing the specificity of approach. We also investigated the mass scaling of isotopic shifts, encountering divergent trends for different structural families.

State-of-the-Art Glycomics Technologies in Glycobiotechnology

Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from R&D till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.

MALDI-MS analysis of disaccharide isomers using graphene oxide as MALDI matrix

Disaccharides are sugars composed of two monosaccharides joined by a glycosidic linkage. The specific properties of a disaccharide depend on the type of the glycosidic linkage and the identity of the two component monosaccharides. In this work, seven disaccharide isomers (gentiobiose, isomaltose, melibiose, lactose, maltose, cellobiose, and sucrose) were analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using a graphene oxide matrix. Each disaccharide was identified by its unique cleavage pattern. To determine the feasibility of quantitative analyses based on specific fragment patterns, mixtures of sucrose with cellobiose or maltose were prepared at different ratios and analyzed by MALDI-MS, where a strong linear correlation was observed between the relative peak intensity of the sucrose fragment peak at m/z 185 and the amount of sucrose in the mixture. The calibration curve was successfully applied to obtain the relative amount of maltose and sucrose in four different honey samples.

Resolving Isomeric Structures of Native Glycans by Nanoflow Porous Graphitized Carbon Chromatography-Mass Spectrometry

Characterization of the structural diversity of glycans by liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains an analytical challenge in large-scale glycomics applications because of the presence of heterogeneous composition, ubiquitous isomers, lability of post-translational glycan modifications, and complexity of data interpretation. High-resolution separation of glycan isomers differentiating from positional, linkage, branching, and anomeric structures is often a prerequisite to ensure the comprehensive glycan identification. Here, we developed a straightforward method using self-packed capillary porous graphitic carbon (PGC) columns for nanoflow LC-MS/MS analyses of native glycans released from glycoproteins. The technique enables highly resolved chromatographic separation of over 20 high-mannose glycan isomers in ribonuclease B and a diverse range of hybrid and complex-type sialoglycoforms of fetuin. The distinct structures of anomeric glycans and linkage sialoglycan isomers, α2,3 and α2,6, were identified by the characteristic MS/MS fragment ions. A glycan sequencing strategy utilizing diagnostic ions and complementary fragments specific to branching residues was established to simplify the MS/MS data interpretation of closely related isomeric structures. To promote the PGC-LC-MS/MS-based method for glycome-wide applications, we extended analyses to native sulfoglycans from the egg-propagated and cell culture-derived influenza vaccines and demonstrate the high-resolution separation and structural characterization of underivatized neutral and anionic glycoforms including oligomannosidic glycan anomers, sialoglycan linkage isomers, and regioisomers of afucosylated and fucosylated sulfoglycans containing sulfated-6-GlcNAc and sulfated-4-GalNAc residues.

Discrimination of isomeric trisaccharides and their relative quantification in honeys using trapped ion mobility spectrometry

Carbohydrates play a myriad of critical roles as key intermediaries for energy storage, cell wall constituents, or also fuel for organisms. The deciphering of multiple structural isomers based on the monosaccharides composition (stereoisomers), the type of glycosidic linkages (connectivity) and the anomeric configuration (α and β), remains a major analytical challenging task. The possibility to discriminate 13 underivatized isomeric trisaccharides were reported using electrospray ionization coupled to trapped ion mobility spectrometry (ESI-TIMS). After optimization of scan ratio enhancing both the mobility resolving power (R) and resolution (r), fingerprints from 5 different honeys were obtained. Seven trisaccharides with relative content varying from 1.5 to 58.3%, were identified. It was demonstrated that their relative content and/or their ratio could be used to ascertain origin of the honeys. Moreover, such direct approach constitutes an alternative tool to current longer chromatographic runs, paving the way to a transfer as suitable routine analysis.

High-Resolution Ion Mobility Separations of Isomeric Glycoforms with Variations on the Peptide and Glycan Levels

Glycosylation is a ubiquitous post-translational modification (PTM) that strongly affects the protein folding and function. Glycosylation patterns are impacted by many diseases, making promising biomarkers. Glycans are also the most complex PTMs, exhibiting isomers (linkage, anomers, and those with isomeric moieties). Permuted with localization variants that occur for all PTMs, these produce numerous isomeric glycoforms. Characterizing them by mass spectrometry and ion mobility spectrometry (IMS) has been a challenge. High-definition differential IMS (FAIMS) had robustly disentangled isomeric peptides involving other PTMs but was not evaluated for glycopeptides that featured multilevel isomerism. Here, we apply it to representative mucin glycopeptides with O-linked glycans: three GalNAc localization variants, a pair with α/β GalNAc anomers, and another with GalNAc/GlcNAc isomers. The first two classes were separated baseline with the resolution exceeding previous benchmarks by 10-fold, and the last pair was partly resolved. The recently demonstrated straightforward coupling to ultrahigh-resolution MS and electron-transfer dissociation makes high-definition FAIMS an attractive tool for glycoproteomics.

An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry

Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.

Separation of Sialylated Glycan Isomers by Differential Mobility Spectrometry

Mass spectrometry has proven itself to be an important technology for characterizing intact glycoproteins, glycopeptides, and released glycans. However, these molecules often present significant challenges during analysis. For example, glycans of identical molecular weights can be present in many isomeric forms, with one form having dramatically more biological activity than the others. Discriminating among these isomeric forms using mass spectrometry alone can be daunting, which is why orthogonal techniques, such as ion mobility spectrometry, have been explored. Here, we demonstrate the use of differential mobility spectrometry (DMS) to separate isomeric glycans differing only in the linkages of sialic acid groups (e.g., α 2,3 versus α 2,6). This ability extends from a small trisaccharide species to larger biantennary systems and is driven, in part, by the role of intramolecular solvation of the charge site(s) on these ions within the DMS environment.

Systematic Isolation and Structure Elucidation of Urinary Metabolites Optimized for the Analytical-Scale Molecular Profiling Laboratory

Annotation and identification of metabolite biomarkers is critical for their biological interpretation in metabolic phenotyping studies, presenting a significant bottleneck in the successful implementation of untargeted metabolomics. Here, a systematic multistep protocol was developed for the purification and de novo structural elucidation of urinary metabolites. The protocol is most suited for instances where structure elucidation and metabolite annotation are critical for the downstream biological interpretation of metabolic phenotyping studies. First, a bulk urine pool was desalted using ion-exchange resins enabling large-scale fractionation using precise iterations of analytical scale chromatography. Primary urine fractions were collected and assembled into a “fraction bank” suitable for long-term laboratory storage. Secondary and tertiary fractionations exploited differences in selectivity across a range of reversed-phase chemistries, achieving the purification of metabolites of interest yielding an amount of material suitable for chemical characterization. To exemplify the application of the systematic workflow in a diverse set of cases, four metabolites with a range of physicochemical properties were selected and purified from urine and subjected to chemical formula and structure elucidation by respective magnetic resonance mass spectrometry (MRMS) and NMR analyses. Their structures were fully assigned as tetrahydropentoxyline, indole-3-acetic-acid-O-glucuronide, p-cresol glucuronide, and pregnanediol-3-glucuronide. Unused effluent was collected, dried, and returned to the fraction bank, demonstrating the viability of the system for repeat use in metabolite annotation with a high degree of efficiency.

Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations

We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path with extending routing (SLIM SUPER) ion mobility-mass spectrometry (IM-MS) for the unambiguous annotation of important isomeric glycoforms in carbon-fixing communities.

Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses

Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man₈GlcNAc₂ isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

Rapid resolution of carbohydrate isomers via multi-site derivatization ion mobility-mass spectrometry

Identifying small sugar isomers can be challenging by ion mobility-mass spectrometry (IM-MS) alone due to their small collision cross section differences.

Cyclodextrin and malto-dextrose collision cross sections determined in a drift tube ion mobility mass spectrometer using nitrogen bath gas

Ion mobility measurements indicate unique distributions for cyclodextrin ions.

Anomeric memory of the glycosidic bond upon fragmentation and its consequences for carbohydrate sequencing

Deciphering the carbohydrate alphabet is problematic due to its unique complexity among biomolecules. Strikingly, routine sequencing technologies-which are available for proteins and DNA and have revolutionised biology-do not exist for carbohydrates. This lack of structural tools is identified as a crucial bottleneck, limiting the full development of glycosciences and their considerable potential impact for the society. In this context, establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here we show that a hybrid analytical approach integrating molecular spectroscopy with mass spectrometry provides an adequate metric to resolve carbohydrate isomerisms, i.e the monosaccharide content, anomeric configuration, regiochemistry and stereochemistry of the glycosidic linkage. On the basis of the spectroscopic discrimination of MS fragments, we report the unexpected demonstration of the anomeric memory of the glycosidic bond upon fragmentation. This remarkable property is applied to de novo sequencing of underivatized oligosaccharides.Establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here the authors show a hybrid analytical approach integrating molecular spectroscopy and mass spectrometry to resolve carbohydrate isomerism, anomeric configuration, regiochemistry and stereochemistry.

Glycosaminoglycan Analysis by Cryogenic Messenger-Tagging IR Spectroscopy Combined with IMS-MS

We combine ion mobility spectrometry with cryogenic, messenger-tagging, infrared spectroscopy and mass spectrometry to identify different isomeric disaccharides of chondroitin sulfate (CS) and heparan sulfate (HS), which are representatives of two major subclasses of glycosaminoglycans. Our analysis shows that while CS and HS disaccharide isomers have similar drift times, they can be uniquely distinguished by their vibrational spectrum between ∼3200 and 3700 cm-1 due to their different OH hydrogen-bonding patterns. We suggest that this combination of techniques is well suited to identify and characterize glycan isomers directly, which presents tremendous challenges for existing methods.

Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry

Differentiating the structure of isobaric glycopeptides represents a major challenge for mass spectrometry-based characterisation techniques. Here we show that the regiochemistry of the most common N-acetylneuraminic acid linkages of N-glycans can be identified in a site-specific manner from individual glycopeptides using ion mobility-mass spectrometry analysis of diagnostic fragment ions.

Travelling-wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N-glycans

Nitrogen collisional cross sections (CCSs) of hybrid and complex glycans released from the glycoproteins IgG, gp120 (from human immunodeficiency virus), ovalbumin, α1-acid glycoprotein and thyroglobulin were measured with a travelling-wave ion mobility mass spectrometer using dextran as the calibrant. The utility of this instrument for isomer separation was also investigated. Some isomers, such as Man₃ GlcNAc₃ from chicken ovalbumin and Man₃ GlcNAc₃ Fuc₁ from thyroglobulin could be partially resolved and identified by their negative ion fragmentation spectra obtained by collision-induced decomposition (CID). Several other larger glycans, however, although existing as isomers, produced only asymmetric rather than separated arrival time distributions (ATDs). Nevertheless, in these cases, isomers could often be detected by plotting extracted fragment ATDs of diagnostic fragment ions from the negative ion CID spectra obtained in the transfer cell of the Waters Synapt mass spectrometer. Coincidence in the drift times of all fragment ions with an asymmetric ATD profile in this work, and in the related earlier paper on high-mannose glycans, usually suggested that separations were because of conformers or anomers, whereas symmetrical ATDs of fragments showing differences in drift times indicated isomer separation. Although some significant differences in CCSs were found for the smaller isomeric glycans, the differences found for the larger compounds were usually too small to be analytically useful. Possible correlations between CCSs and structural types were also investigated, and it was found that complex glycans tended to have slightly smaller CCSs than high-mannose glycans of comparable molecular weight. In addition, biantennary glycans containing a core fucose and/or a bisecting GlcNAc residue fell on different mobility-m/z trend lines to those glycans not so substituted with both of these substituents contributing to larger CCSs. Copyright © 2016 John Wiley & Sons, Ltd.

Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry

Detailed structural elucidation of protein glycosylation is a tedious process often involving several techniques. Glycomics and glycoproteomics approaches with mass spectrometry offer a rapid platform for glycan profiling but are limited by the inability to resolve isobaric species such as linkage and positional isomers. Recently, ion mobility spectrometry (IMS) has been shown to effectively resolve isobaric oligosaccharides, but the utility of IMS to obtain glycan structural information on a site-specific level with proteomic analyses has yet to be investigated. Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. With further development IMS may hold the potential for rapid and complete structural elucidation of glycan chains at a site-specific level.

Separation and Identification of Isomeric Glycans by Selected Accumulation-Trapped Ion Mobility Spectrometry-Electron Activated Dissociation Tandem Mass Spectrometry

One of the major challenges in structural characterization of oligosaccharides is the presence of many structural isomers in most naturally occurring glycan mixtures. Although ion mobility spectrometry (IMS) has shown great promise in glycan isomer separation, conventional IMS separation occurs on the millisecond time scale, largely restricting its implementation to fast time-of-flight (TOF) analyzers which often lack the capability to perform electron activated dissociation (ExD) tandem MS analysis and the resolving power needed to resolve isobaric fragments. The recent development of trapped ion mobility spectrometry (TIMS) provides a promising new tool that offers high mobility resolution and compatibility with high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometers when operated under the selected accumulation-TIMS (SA-TIMS) mode. Here, we present our initial results on the application of SA-TIMS-ExD-FTICR MS to the separation and identification of glycan linkage isomers.

Fragmentation and ion mobility properties of negative ions from N-linked carbohydrates: Part 7. Reduced glycans

RATIONALE

Negative ion collision-induced dissociation (CID) spectra of released N-glycans provide very informative structural information relating to branching patterns and location of residues such as fucose. For some structural studies, particularly those involving chromatography, glycans are often reduced to avoid production of multiple peaks from α- and β-anomers. We examined the effect of reduction on the production of diagnostic fragment ions and on the ion mobility properties of N-glycans.

METHODS

Released N-glycans from the glycoproteins bovine fetuin, ribonuclease B, chicken ovalbumin, and porcine thyroglobulin were reduced with sodium cyanoborohydride and both negative ion CID spectra and ion mobility properties of their phosphate adducts were examined with a Waters Synapt G2Si travelling-wave ion mobility mass spectrometer with electrospray sample introduction. Estimated collisional cross sections were measured with dextran as the calibrant,

RESULTS

Fragment ions were similar to those from the unreduced glycans with the exception that the prominent (2,4) A cleavage ion from the reducing terminus was replaced by a prominent [M-H3 PO4](-) ion. Other ions arising from the chitobiose core were of lower relative abundance than those from the unreduced glycans. Estimated collisional cross sections were similar to those of the unreduced compounds but with symmetrical arrival time distribution (ATD) profiles, unlike those of the unreduced glycans whose peaks often contained prominent asymmetry. This observation showed that this asymmetry was due to anomer separation.

CONCLUSIONS

Reduction of the reducing terminal GlcNAc residue resulted in fewer diagnostic ions from the chitobiose core but fragmentation of the remainder of the molecules generally paralleled that of the unreduced glycans. Thus, most structural information, with the exception of the linkage position of fucose on the core GlcNAc, was available. ATD peaks were symmetrical with the result that cross sections were more appropriate for data-base searching than those from the non-reduced compounds where asymmetry produced lower precision in the measurement.

Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans

The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed.

Ion Mobility in Clinical Analysis: Current Progress and Future Perspectives

BACKGROUND

Ion mobility spectrometry (IMS) is a rapid separation tool that can be coupled with several sampling/ionization methods, other separation techniques (e.g., chromatography), and various detectors (e.g., mass spectrometry). This technique has become increasingly used in the last 2 decades for applications ranging from illicit drug and chemical warfare agent detection to structural characterization of biological macromolecules such as proteins. Because of its rapid speed of analysis, IMS has recently been investigated for its potential use in clinical laboratories.

CONTENT

This review article first provides a brief introduction to ion mobility operating principles and instrumentation. Several current applications will then be detailed, including investigation of rapid ambient sampling from exhaled breath and other volatile compounds and mass spectrometric imaging for localization of target compounds. Additionally, current ion mobility research in relevant fields (i.e., metabolomics) will be discussed as it pertains to potential future application in clinical settings.

SUMMARY

This review article provides the authors' perspective on the future of ion mobility implementation in the clinical setting, with a focus on ambient sampling methods that allow IMS to be used as a “bedside” standalone technique for rapid disease screening and methods for improving the analysis of complex biological samples such as blood plasma and urine.