Identification of Mobility-Resolved N-Glycan Isomers

Impact of glycosylation on viral vaccines

Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.

Probing High-Order Transient Oligomers Using Ion Mobility Mass Spectrometry Coupled with Infrared Action Spectroscopy

Understanding and controlling peptide aggregation are critical due to its neurotoxic implications. However, structural information about the key intermediates, the oligomers, is obscured by a cascade of coinciding events occurring at various time and energy scales, which results in complex and heterogeneous mixtures of oligomers. To address this challenge, we have developed the Photo-Synapt, a novel, multidimensional spectrometer that integrates ion mobility mass spectrometry with infrared (IR) action spectroscopy within a single experiment. By combining three different orthogonal analytical dimensions, we can select and isolate individual oligomers by mass, charge, size, and shape and provide a unique molecular fingerprint for each oligomer. The broad application of this technology is demonstrated by its application to oligosaccharide analysis from glycoproteins, which are challenging to analyze due to the minute differences between isomers. By integration of IR action spectroscopy with ion mobility mass spectrometry, this approach adds an analytical dimension that effectively addresses this limitation, offering a unique molecular fingerprint for each isomer.

Development of a cyclic ion mobility spectrometry-mass spectrometry-based collision cross-section database of permethylated human milk oligosaccharides

Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain-gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons - there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High-resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed-phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first-ever high-resolution collision cross-section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high-resolution cyclic ion mobility spectrometry-mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography-tandem mass spectrometry-based methods.

Recent advances in high-resolution traveling wave-based ion mobility separations coupled to mass spectrometry

Recently, ion mobility spectrometry-mass spectrometry (IMS-MS) has become more readily incorporated into various omics-based workflows. These growing applications are due to developments in instrumentation within the last decade that have enabled higher-resolution ion mobility separations. Two such platforms are the cyclic (cIMS) and structures for lossless ion manipulations (SLIM), both of which use traveling wave ion mobility spectrometry (TWIMS). High-resolution separations achieved with these techniques stem from the drastically increased pathlengths, on the order of 10 s of meters to >1 km, in both cIMS-MS and SLIM IMS-MS, respectively. Herein, we highlight recent developments and advances, for the period 2019-2023, in high-resolution traveling wave-based IMS-MS through instrumentation, calibration strategies, hyphenated techniques, and applications. Specifically, we will discuss applications including CCS calculations in multipass IMS-MS separations, coupling of IMS-MS with chromatography, imaging, and cryogenic infrared spectroscopy, and isomeric separations of glycans, lipids, and other small metabolites.

Serum N-Glycan Profiling of Patients with Narcolepsy Type 1 Using LC-MS/MS

The neurological condition known as narcolepsy type 1 (NT1) is an uncommon condition marked by extreme daytime sleepiness, cataplexy, sleep paralysis, hallucinations, disrupted nocturnal sleep, and low or undetectable levels of orexin in the CSF fluid. NT1 has been hypothesized to be an immunological disorder; its treatment is currently only symptomatic, and misdiagnosis is not uncommon. This study compares the N-glycome of NT1 patients with healthy controls in search of potential glycan biomarkers using LC-MS/MS. A total of 121 candidate N-glycans were identified, 55 of which were isomeric N-glycan structures and 65 were not. Seventeen N-glycan biomarker candidates showed significant differences between the NT1 and control cohorts. All of the candidate glycan biomarkers were isomeric except HexNAc6Hex7Fuc0NeuAc1 (6701) and HexNAc6Hex7Fuc1NeuAc2 (6712). Therefore, with isomeric and nonisomeric structures, a total of 20 candidate N-glycan biomarkers are reported in this study, and interestingly, all are either sialylated or sialylated-fucosylated and upregulated in NT1 relative to the control. The distribution levels of all the identified N-glycans show that the sialylated glycan type is the most abundant in NT1 and is majorly disialylated, although the trisialylated subtype is three-fold higher in NT1 compared to the healthy control. The first isomers of HexNAc5Hex6Fuc0NeuAc3 (5603), HexNAc6Hex7Fuc0NeuAc2 (6702), and HexNAc6Hex7Fuc1NeuAc4 (6714) expressed a high level of fold changes (FC) of 1.62, 2.19, and 2.98, respectively. These results suggest a different N-glycome profile of NT1 and a relationship between sialylated glycan isomers in NT1 disease development or progression. The revelation of N-glycan expression alterations in this study may improve NT1 diagnostic methods, understanding of NT1 pathology, and the development of new targeted therapeutics.

Strategy strengthens structural identification through hyphenating full collision energy ramp-MS2 and full exciting energy ramp-MS3 spectra: An application for metabolites identification of rosmarinic acid

"MS/MS spectrum to structure" analysis is the most challenging task for MS/MS-relied qualitative characterization. The conventional database- and computation-assisted strategies cannot reach confirmative identification, notably for isomers. Hence, an advanced strategy was proposed here through tackling the two determinant obstacles such as the transformation from elemental compositions to fragment ion structures and the linkage style amongst substructures. As typical conjugated structures, esters were measured for strategy illustration, and metabolite identification of a famous natural antioxidant namely rosmarinic acid (RosA) in rat was undertaken for applicability justification. Through programming online energy-resolved (ER)-MS for the first collision cell of Qtrap-MS device, full collision energy ramp (FCER)-MS2 spectrum was configured for [M-H]- ion of each ester to provide optimal collision energies (OCEs) for all concerned diagnostic fragment ions (DFIs), i.e. a-, b-, c-, y-, and z-type ions. The linear correlations between masses and OCEs were built for each ion type to facilitate DFIs recognition from chaotic MS2 spectrum. To identify 1st-generation fragment ions, full exciting energy ramp (FEER)-MS3 spectra were configured for key DFIs via programming the second ER-MS in the latter collision chamber. FEER-MS3 spectrum of 1st-generation fragment ion for ester was demonstrated to be identical with FEER-MS2 spectrum of certain hydrolysis product when sharing the same structure. After applying the advanced strategy to recognize DFIs and identify 1st-generation fragment ions, a total of forty metabolites (M1-M40), resulted from hydrolysis, methylation, sulfation, and glucuronidation, were unambiguously identified for RosA after oral administration. Together, the advanced bottom-up strategy hyphenating FCER-MS2 and FEER-MS3 spectra, is meaningful to strengthen "MS/MS spectrum to structure" analysis through recognizing and identifying fragment ions.

Top-down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms

Enzymatic catalysis is one of the fundamental processes that drives the dynamic landscape of post-translational modifications (PTMs), expanding the structural and functional diversity of proteins. Here, we assessed enzyme specificity using a top-down ion mobility spectrometry (IMS) and tandem mass spectrometry (MS/MS) workflow. We successfully applied trapped IMS (TIMS) to investigate site-specific N-ε-acetylation of lysine residues of full-length histone H4 catalyzed by histone lysine acetyltransferase KAT8. We demonstrate that KAT8 exhibits a preference for N-ε-acetylation of residue K16, while also adding acetyl groups on residues K5 and K8 as the first degree of acetylation. Achieving TIMS resolving power values of up to 300, we fully separated mono-acetylated regioisomers (H4K5ac, H4K8ac, and H4K16ac). Each of these separated regioisomers produce unique MS/MS fragment ions, enabling estimation of their individual mobility distributions and the exact localization of the N-ε-acetylation sites. This study highlights the potential of top-down TIMS-MS/MS for conducting enzymatic assays at the intact protein level and, more generally, for separation and identification of intact isomeric proteoforms and precise PTM localization.

Combining Liquid Chromatography and Cryogenic IR Spectroscopy in Real Time for the Analysis of Oligosaccharides

While the combination of liquid chromatography (LC) and mass spectrometry (MS) serves as a robust approach for oligosaccharide analysis, it has difficulty distinguishing the smallest differences between isomers. The integration of infrared (IR) spectroscopy within a mass spectrometer as an additional analytical dimension can effectively address this limitation by providing a molecular fingerprint that is unique to each isomer. However, the direct interfacing of LC-MS with IR spectroscopy presents a technical challenge arising from the mismatch in the operational time scale of each method. In previous studies, this temporal incompatibility was mitigated by employing strategies designed to slow down or broaden the LC elution peaks of interest, but this workaround is applicable only for a few species at a time, necessitating multiple LC runs for comprehensive analysis. In the current work, we directly couple LC with cryogenic IR spectroscopy by acquiring a spectrum in as little as 10 s. This allows us to generate an orthogonal data dimension for molecular identification in the same amount of time that it normally takes for LC analysis. We successfully demonstrate this approach on a commercially available human milk oligosaccharide product, acquiring spectral information on the eluting peaks in real time and using it to identify both the specified constituents and nonspecified product impurities.

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

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

An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.

General Method to Obtain Collision Cross-Section Values in Multipass High-Resolution Cyclic Ion Mobility Separations

In recent years, ion mobility spectrometry-mass spectrometry (IMS-MS) has advanced the field of omics-based research, especially with the development of high-resolution platforms; however, these separations have generally been qualitative in nature. The rotationally averaged ion neutral collision cross section (CCS) is one of the only quantitative metrics available for aiding in characterizing biomolecules in IMS-MS. However, determining the CCS of an ion for multipass IMS systems, such as in cyclic ion mobility-mass spectrometry (cIMS-MS) and structures for lossless ion manipulations, has been challenging due to the lack of methods available for calculating CCS when more than a single pass is required for separation as well as the laborious nature of requiring calibrants and unknown compounds to be subjected to identical number of passes, which may not be possible in certain instances because of peak splitting, high levels of diffusion, etc. Herein, we present a general method that uses average ion velocities for calculating CCS values in cIMS-MS-based separations. Initially, we developed calibration curves using common CCS calibrants [i.e., tetra-alkylammonium salts, polyalanine, and hexakis(fluoroalkoxy)phosphazines] at different traveling wave (TW) conditions and the calculated cIMS CCS values were within ∼1% error or less compared to previously established drift tube IMS CCS measurements. Since it has been established that glycans can split into their α/β anomers, we utilized this method for two glycan species, 2α-mannobiose and melibiose. Both glycans were analyzed at the same TW conditions as the calibrants, and we observed anomer splitting at pathlengths of 20 m for 2α-mannobiose and 40 m for melibiose and thus assigned two unique CCS values for each glycan, which is the first time this has ever been done. We have demonstrated that the use of average ion velocities is a robust approach for obtaining CCS values with good agreement to CCS measurements from the previous literature and anticipate that this methodology can be applied to any IMS-MS platform that utilizes multipass separations. Our future work aims to incorporate this methodology for the development of a high-resolution CCS database to aid in the characterization of human milk oligosaccharides.

Multistage Ion Mobility Spectrometry Combined with Infrared Spectroscopy for Glycan Analysis

The structural complexity of glycans makes their characterization challenging, not only because of the presence of various isomeric forms of the precursor molecule but also because the fragments can themselves be isomeric. We have recently developed an IMS-CID-IMS approach using structures for lossless ion manipulations (SLIM) combined with cryogenic infrared (IR) spectroscopy for glycan analysis. It allows mobility separation and collision-induced dissociation of a precursor glycan followed by mobility separation and IR spectroscopy of the fragments. While this approach holds great promise for glycan analysis, we often encounter fragments for which we have no standards to identify their spectroscopic fingerprint. In this work, we perform proof-of-principle experiments employing a multistage SLIM-based IMS-CID technique to generate second-generation fragments, followed by their mobility separation and spectroscopic interrogation. This approach provides detailed structural information about the first-generation fragments, including their anomeric form, which in turn can be used to identify the precursor glycan.

Assessing the Use of Host-Guest Chemistry in Conjunction with Cyclic Ion Mobility Separations for the Linkage-Specific Characterization of Human Milk Oligosaccharides

Human milk oligosaccharides (HMOs) are a class of glycans that are highly abundant in human milk and contribute to the healthy growth of an infant's immune system. While new advancements in analytical methodologies have been made in glycomics, the high degree of isomeric heterogeneity and lack of authentic standards have made the high-resolution separation and accurate characterization of linkage positioning of all HMO species very challenging. Herein, we present an evaluation of the use of host-guest chemistry in conjunction with cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based separations for the identification of linkage positioning in three pairs of di-, tetra-, and hexasaccharide HMO isomers that only differ in the positioning of one glycosidic linkage (β1,3 versus β1,4). Suitable hosts, such as α/β cyclodextrins, cucurbit[n]urils (n = 5, 7), crown ethers, cyclic peptides, and an ionophore, were used to assess host-guest inclusion complex formation as well as linkage-specific cIMS-MS trends. Our results indicated a linkage-specific trend for the [M + 2α + 2H]2+ cyclodextrin-based host-guest inclusion complexes where the β1,3 linkage-containing isomers were always higher mobility than the β1,4 linkage-containing ones as well one for the [M + α + β + 2H]2+ complexes where the β1,4 linkage-containing isomers were always higher mobility than the β1,3 linkage-containing ones. We also observed diagnostic mobility fingerprints for the cucurbituril-based complexes. We anticipate that linkage-specific and mobility fingerprint trends can potentially aid in identifying linkage positioning for other HMO isomers as well as in complex human milk samples.