High-field asymmetric-waveform ion mobility spectrometry and electron detachment dissociation of isobaric mixtures of glycosaminoglycans

Development of mass spectrometric glycan characterization tags using acid-base chemistry and/or free radical chemistry

Despite recent advances in glycomics, glycan characterization still remains an analytical challenge. Accordingly, numerous glycan-tagging reagents with different chemistries were developed, including those involving acid-base chemistry and/or free radical chemistry. Acid-base chemistry excels at dissociating glycans into their constituent components in a systematic and predictable manner to generate cleavages at glycosidic bonds. Glycans are also highly susceptible to depolymerization by free radical processes, which is supported by results observed from electron-activated dissociation techniques. Therefore, the free radical activated glycan sequencing (FRAGS) reagent was developed so as to possess the characteristics of both acid-base and free radical chemistry, thus generating information-rich glycosidic bond and cross-ring cleavages. Alternatively, the free radical processes can be induced via photodissociation of the specific carbon-iodine bond which gives birth to similar fragmentation patterns as the FRAGS reagent. Furthermore, the methylated-FRAGS (Me-FRAGS) reagent was developed to eliminate glycan rearrangements by way of a fixed charged as opposed to a labile proton, which would otherwise yield additional, yet unpredictable, fragmentations including internal residue losses or multiple external residue losses. Lastly, to further enhance glycan enrichment and characterization, solid-support FRAGS was developed.

High-resolution ion mobility spectrometry-mass spectrometry for isomeric separation of prostanoids after Girard's reagent T derivatization

RATIONALE

Isomeric separation of prostanoids is often a challenge and requires chromatography and time-consuming sample preparation. Multiple prostanoid isomers have distinct in vivo functions crucial for understanding the inflammation process, including prostaglandins E₂ (PGE₂ ) and D₂ (PGD₂ ). High-resolution ion mobility spectrometry (IMS) based on linear ion transport in low-to-moderate electric fields and nonlinear ion transport in strong electric fields emerges as a broad approach for rapid separations prior to mass spectrometry.

METHODS

Derivatization with Girard's reagent T (GT) was used to overcome inefficient ionization of prostanoids in negative ionization mode due to poor deprotonation of the carboxylic acid group. Three high-resolution IMS techniques, namely linear cyclic IMS, linear trapped IMS, and nonlinear high-field asymmetric waveform IMS, were compared for the isomeric separation and endogenous detection of prostanoids present in intestinal tissue.

RESULTS

Direct infusion of GT-derivatized prostanoids proved to increase the ionization efficiency in positive ionization mode by a factor of >10, which enabled detection of these molecules in endogenous concentration levels. The high-resolution IMS comparison revealed its potential for rapid isomeric analysis of biologically relevant prostanoids. Strengths and weaknesses of both linear and nonlinear IMS are discussed. Endogenous prostanoid detection in intestinal tissue extracts demonstrated the applicability of our approach in biomedical research.

CONCLUSIONS

The applied derivatization strategy offers high sensitivity and improved stereoisomeric separation for screening of complex biological systems. The high-resolution IMS comparison indicated that the best sensitivity and resolution are achieved by linear and nonlinear IMS, respectively.

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.

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.

Commercial Low Molecular Weight Heparins - Patent Ecosystem and Technology Paradigm for Quality Characterization

Heparin is a subject of ever-growing interest for laboratory researchers and pharmaceutical industry. One of the driving factors is its critical life-saving drug status, which during the COVID-19 pandemic has assumed a central role in disease treatment and/or prevention. Apart, heparin is one amongst few drugs enjoying a "demand constant" status. In 2020, heparin market size was valued to US$6.5 bn., and given the ongoing stability in the COVID-19 health crisis, it is expected to reach US$11.43 bn. by 2027 with yearly growth rate momentum (CAGR) of 3.9% during the forecast period (Pepi et al., Mol Cell Proteomics 20:100,025, 2021). As patent is a limited monopoly, every year, many patents on low molecular weight heparin (LMWH; a chemically or enzymatically degraded product of unfractionated heparin) are losing market exclusivity worldwide, inviting the generic/biosimilar drug manufacturers to capture market share with cheaper drug products. By tracking patent expiration, drugs in patent litigation, regulatory setbacks for innovator companies (such as those seeking data exclusivity or patent term extension), or other unexpected events affecting market demand and competition, generics can make investment decisions in manufacturing off-patent LMWH drug products of commercial significance. However, given the US Food and Drug Administration (FDA), European Medicine Agency (EMA), Drug Regulatory Authority of Pakistan (DRAP), and other regulatory authorities scientifically rigorous standards for generic/biosimilar LMWH drug products marketing approval, the market is secured and momentous for drug makers that could demonstrate through scientific and clinical dataset that the generic/biosimilar LMWH drug product is of the same quality and purity as the innovator drug product. This study presents an overview of the patent landscape of commercially available LMWHs and advanced analytical techniques for their structural and biochemical characterization for quality control and quality assurance during manufacturing and post-marketing. The study also covers FDA, EMA, Health Canada, and DRAP's current approaches to evaluating the generic/biosimilar LMWH drug products for quality, safety including immunogenicity, and efficacy.

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.

Resolving Heparan Sulfate Oligosaccharide Positional Isomers Using Hydrophilic Interaction Liquid Chromatography-Cyclic Ion Mobility Mass Spectrometry

Heparan sulfate (HS) is a linear polysaccharide covalently attached to proteoglycans on cell surfaces and within extracellular matrices in all animal tissues. Many biological processes are triggered by the interactions among HS binding proteins and short structural motifs in HS chains. The determination of HS oligosaccharide structures using liquid chromatography-mass spectrometry (LC-MS) is made challenging by the existence of positional sulfation and acetylation isomers. The determination of uronic acid epimer positions is even more challenging. While hydrophilic interaction liquid chromatography (HILIC) separates HS saccharides based on their composition, there is a very limited resolution of positional isomers. This lack of resolution places a burden on the tandem mass spectrometry step for assigning saccharide isomers. In this work, we explored the use of the ion mobility dimension to separate HS saccharide isomers based on molecular shape in the gas phase. We showed that the combination of HILIC and cyclic ion mobility mass spectrometry (cIM-MS) was extremely useful for resolving HS positional isomers including uronic acid epimers and sulfate positions. Furthermore, HILIC-cIM-MS differentiated multicomponent HS isomeric saccharide mixtures. In summary, HILIC-cIM-MS provided high-quality data for analysis of HS oligosaccharide isomeric mixtures that may prove useful in the discovery of new structural motifs for HS binding proteins and for the targeted quality control analysis of commercial HS products.

Analysis of the Glycosaminoglycan Chains of Proteoglycans

Glycosaminoglycans (GAGs) are heterogeneous, negatively charged, macromolecules that are found in animal tissues. Based on the form of component sugar, GAGs have been categorized into four different families: heparin/heparan sulfate, chondroitin/dermatan sulfate, keratan sulfate, and hyaluronan. GAGs engage in biological pathway regulation through their interaction with protein ligands. Detailed structural information on GAG chains is required to further understanding of GAG-ligand interactions. However, polysaccharide sequencing has lagged behind protein and DNA sequencing due to the non-template-driven biosynthesis of glycans. In this review, we summarize recent progress in the analysis of GAG chains, specifically focusing on techniques related to mass spectroscopy (MS), including separation techniques coupled to MS, tandem MS, and bioinformatics software for MS spectrum interpretation. Progress in the use of other structural analysis tools, such as nuclear magnetic resonance (NMR) and hyphenated techniques, is included to provide a comprehensive perspective.

Volatile Metabolic Markers for Monitoring Pectobacterium carotovorum subsp. carotovorum Using Headspace Solid-Phase Microextraction Coupled with Gas Chromatography-Mass Spectrometry

Identifying the extracellular metabolites of microorganisms in fresh vegetables is industrially useful for assessing the quality of processed foods. Pectobacterium carotovorum subsp. carotovorum (PCC) is a plant pathogenic bacterium that causes soft rot disease in cabbages. This microbial species in plant tissues can emit specific volatile molecules with odors that are characteristic of the host cell tissues and PCC species. In this study, we used headspace solid-phase microextraction followed by gas chromatography coupled with mass spectrometry (HS-SPME-GC-MS) to identify volatile compounds (VCs) in PCC-inoculated cabbage at different storage temperatures. HS-SPME-GC-MS allowed for recognition of extracellular metabolites in PCC-infected cabbages by identifying specific volatile metabolic markers. We identified 4-ethyl-5-methylthiazole and 3-butenyl isothiocyanate as markers of fresh cabbages, whereas 2,3-butanediol and ethyl acetate were identified as markers of soft rot in PCC-infected cabbages. These analytical results demonstrate a suitable approach for establishing non-destructive plant pathogen-diagnosis techniques as alternatives to standard methods, within the framework of developing rapid and efficient analytical techniques for monitoring plant-borne bacterial pathogens. Moreover, our techniques could have promising applications in managing the freshness and quality control of cabbages.

Mammal Hyaluronidase Activity on Chondroitin Sulfate and Dermatan Sulfate: Mass Spectrometry Analysis of Oligosaccharide Products

Mammalian hyaluronidases are endo-N-acetyl-D-hexosaminidases involved in the catabolism of hyaluronic acid (HA) but their role in the catabolism of chondroitin sulfate (CS) is also examined. HA and CS are glycosaminoglycans (GAGs) implicated in several physiological and pathological processes, and understanding their metabolism is of significant importance. Data have been previously reported on the degradation of CS under the action of hyaluronidase, yet a detailed structural investigation of CS depolymerization products remains necessary to improve our knowledge of the CS depolymerizyng activity of hyaluronidase. For that purpose, the fine structural characterization of CS oligosaccharides formed upon the enzymatic depolymerization of various CS sub-types by hyaluronidase has been carried out by high resolution Orbitrap mass spectrometry and extreme UV (XUV) photodissociation tandem mass spectrometry. The exact mass measurements show the formation of wide size range of even oligosaccharides upon digestion of CS-A and CS-C comprising hexa- and octa-saccharides among the main digestion products, as well as formation of small quantities of odd-numbered oligosaccharides, while no hyaluronidase activity was detected on CS-B. In addition, slight differences have been observed in the distribution of oligosaccharides in the digestion mixture of CS-A and CS-C, the contribution of longer oligosaccharides being significantly higher for CS-C. The sequence of CS oligosaccharide products determined XUV photodissociation experiments verifies the selective β(1 → 4) glycosidic bond cleavage catalyzed by mammal hyaluronidase. The ability of the mammal hyaluronidase to produce hexa- and higher oligosaccharides supports its role in the catabolism of CS anchored to membrane proteoglycans and in extra-cellular matrix.

Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), online separations, and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs.

GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model

The sulfated glycosaminoglycans (GAGs) are long, linear polysaccharide chains that are typically found as the glycan portion of proteoglycans. These GAGs are characterized by repeating disaccharide units with variable sulfation and acetylation patterns along the chain. GAG length and modification patterns have profound impacts on growth factor signaling mechanisms central to numerous physiological processes. Electron activated dissociation tandem mass spectrometry is a very effective technique for assigning the structures of GAG saccharides; however, manual interpretation of the resulting complex tandem mass spectra is a difficult and time-consuming process that drives the development of computational methods for accurate and efficient sequencing. We have recently published GAGfinder, the first peak picking and elemental composition assignment algorithm specifically designed for GAG tandem mass spectra. Here, we present GAGrank, a novel network-based method for determining GAG structure using information extracted from tandem mass spectra using GAGfinder. GAGrank is based on Google's PageRank algorithm for ranking websites for search engine output. In particular, it is an implementation of BiRank, an extension of PageRank for bipartite networks. In our implementation, the two partitions comprise every possible sequence for a given GAG composition and the tandem MS fragments found using GAGfinder. Sequences are given a higher ranking if they link to many important fragments. Using the simulated annealing probabilistic optimization technique, we optimized GAGrank's parameters on ten training sequences. We then validated GAGrank's performance on three validation sequences. We also demonstrated GAGrank's ability to sequence isomeric mixtures using two mixtures at five different ratios.

Free-Radical-Mediated Glycan Isomer Differentiation

The inherent structural complexity and diversity of glycans pose a major analytical challenge to their structural analysis. Radical chemistry has gained considerable momentum in the field of mass spectrometric biomolecule analysis, including proteomics, glycomics, and lipidomics. Herein, seven isomeric disaccharides and two isomeric tetrasaccharides with subtle structural differences are distinguished rapidly and accurately via one-step radical-induced dissociation. The free-radical-activated glycan-sequencing reagent (FRAGS) selectively conjugates to the unique reducing terminus of glycans in which a localized nascent free radical is generated upon collisional activation and simultaneously induces glycan fragmentation. Higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) are employed to provide complementary structural information for the identification and discrimination of glycan isomers by providing different fragmentation pathways to generate informative, structurally significant product ions. Furthermore, multiple-stage tandem mass spectrometry (MS³ CID) provides supplementary and valuable structural information through the generation of characteristic parent-structure-dependent fragment ions.

Cryogenic Infrared Spectroscopy Reveals Structural Modularity in the Vibrational Fingerprints of Heparan Sulfate Diastereomers

Heparan sulfate and heparin are highly acidic polysaccharides with a linear sequence, consisting of alternating glucosamine and hexuronic acid building blocks. The identity of hexuronic acid units shows a variability along their sequence, as d-glucuronic acid and its C5 epimer, l-iduronic acid, can both occur. The resulting backbone diversity represents a major challenge for an unambiguous structural assignment by mass spectrometry-based techniques. Here, we employ cryogenic infrared spectroscopy on mass-selected ions to overcome this challenge and distinguish isomeric heparan sulfate tetrasaccharides that differ only in the configuration of their hexuronic acid building blocks. High-resolution infrared spectra of a systematic set of synthetic heparan sulfate stereoisomers were recorded in the fingerprint region from 1000 to 1800 cm^-1. The experiments reveal a characteristic combination of spectral features for each of the four diastereomers studied and imply structural modularity in the vibrational fingerprints. Strong spectrum-structure correlations were found and rationalized by state-of-the-art quantum chemical calculations. The findings demonstrate the potential of cryogenic infrared spectroscopy to extend the mass spectrometry-based toolkit for the sequencing of heparan sulfate and structurally related biomolecules.

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.

Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides

Despite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a “Shotgun” Ion Mobility Mass Spectrometry Sequencing (SIMMS²) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS² analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS² thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation.

Heparan sulfates (HS) contain functionally relevant structural motifs, but determining their monosaccharide sequence remains challenging. Here, the authors develop an ion mobility mass spectrometry-based method that allows unambiguous characterization of HS sequences and structure-activity relationships.

A Scoring Algorithm for the Automated Analysis of Glycosaminoglycan MS/MS Data

The role of glycosaminoglycans (GAGs) in major biological functions is numerous and diverse, yet structural characterization of them by mass spectrometric techniques proves to be challenging. Characterization of GAG structure from tandem mass spectrometry is a tedious and time-consuming process but one that can be automated in a database-independent, high-throughput fashion through the assistance of software implementing a genetic algorithm (J. Am. Soc. Mass Spectrom. 29, 1802-1911, 2018). This work presents the manner in which this data is interpreted by the software, specifically addressing the development of a scoring algorithm. The significance of glycosidic and cross-ring fragment ions and the implications that specific fragments provide for assigning the positions of modifications are discussed. The scoring algorithm is tested for statistical merit using the widely accepted expectation value as the criterion for quality. Using MS/MS data for well-characterized standards, this scoring approach is shown to assign the correct structure, with a low likelihood (1 in 1012 chances) that the assigned structure matches the data due to random chance. The integrated software that automates the structure assignment is called Glycosaminoglycan-Unambiguous Identification Technology (G-UNIT).

Resin and Magnetic Nanoparticle-Based Free Radical Probes for Glycan Capture, Isolation, and Structural Characterization

By combining the merits of solid supports and free radical activated glycan sequencing (FRAGS) reagents, we develop a multifunctional solid-supported free radical probe (SS-FRAGS) that enables glycan enrichment and characterization. SS-FRAGS comprises a solid support, free radical precursor, disulfide bond, pyridyl, and hydrazine moieties. Thio-activated resin and magnetic nanoparticles (MNPs) are chosen as the solid support to selectively capture free glycans via the hydrazine moiety, allowing for their enrichment and isolation. The disulfide bond acts as a temporary covalent linkage between the solid support and the captured glycan, allowing the release of glycans via the cleavage of the disulfide bond by dithiothreitol. The basic pyridyl functional group provides a site for the formation of a fixed charge, enabling detection by mass spectrometry and avoiding glycan rearrangement during collisional activation. The free radical precursor generates a nascent free radical upon collisional activation and thus simultaneously induces systematic and predictable fragmentation for glycan structure elucidation. A radical-driven glycan deconstruction diagram (R-DECON) is developed to visually summarize the MS² results and thus allow for the assembly of the glycan skeleton, making the differentiation of isobaric glycan isomers unambiguous. For application to a real-world sample, we demonstrate the efficacy of the SS-FRAGS by analyzing glycan structures enzymatically cleaved from RNase-B.

Online Capillary Zone Electrophoresis Negative Electron Transfer Dissociation Tandem Mass Spectrometry of Glycosaminoglycan Mixtures

Glycosaminoglycans (GAGs) are important biological molecules that are highly anionic and occur in nature as complex mixtures. A platform that combines capillary zone electrophoresis (CZE) separations with mass spectrometry (MS) and gas-phase sequencing by using negative electron transfer dissociation (NETD) is shown to be efficacious for the structural analysis of GAG mixtures. CZE is a separation method well suited to the highly negatively charged nature of GAGs. NETD is an electron-based ion activation method that enables the generation of informative fragments with retention of the labile sulfate half-ester modification that determine specific GAG function. Here we combine for the first time NETD and CZE for assigning the structures of GAG oligomers present in mixtures. The speed of ion activation by NETD is found to couple well with the narrow peaks resulting from CZE migration. The platform was optimized with mixtures of GAG tetrasaccharide standards. The potential of the platform is demonstrated by the analysis of enoxaparin, a complex mixture of low molecular weight heparins, which was separated by CZE within 30 minutes and characterized by NETD MS/MS in one online experiment. 37 unique molecular compositions have been identified in enoxaparin using CZE-MS and 9 structures have been assigned with CZE-NETD-MS/MS.

Structural Characterization of Glycosaminoglycan Carbohydrates Using Ultraviolet Photodissociation

Structural characterization of sulfated glycosaminoglycans (GAGs) by mass spectrometry has long been a formidable analytical challenge owing to their high structural variability and the propensity for sulfate decomposition upon activation with low-energy ion activation methods. While derivatization and complexation workflows have aimed to generate informative spectra using low-energy ion activation methods, alternative ion activation methods present the opportunity to obtain informative spectra from native GAG structures. Both electron- and photon-based activation methods, including electron detachment dissociation (EDD), negative electron transfer dissociation (NETD), and extreme ultraviolet photon activation, have been explored previously to overcome the limitations associated with low-energy activation methods for GAGs and other sulfated oligosaccharides. Further, implementation of such methods on high-resolution mass spectrometers has aided the interpretation of the complex spectra generated. Here, we explore ultraviolet photodissociation (UVPD) implemented on an Orbitrap mass spectrometer as another option for structural characterization of GAGs. UVPD spectra for both dermatan and heparan sulfate structures display extensive fragmentation including both glycosidic and cross-ring cleavages with the extent of sulfate retention comparable to that observed by EDD and NETD. In addition, the relatively short activation time of UVPD makes it promising for higher throughput analysis of GAGs in complex mixtures.

Characterization and Quantification of Highly Sulfated Glycosaminoglycan Isomers by Gated-Trapped Ion Mobility Spectrometry Negative Electron Transfer Dissociation MS/MS

Glycosaminoglycans (GAGs) play vital roles in many biological processes and are naturally present as complex mixtures of polysaccharides with tremendous structural heterogeneity, including many structural isomers. Mass spectrometric analysis of GAG isomers, in particular highly sulfated heparin (Hep) and heparan sulfate (HS), is challenging because of their structural similarity and facile sulfo losses during analysis. Herein, we show that highly sulfated Hep/HS isomers may be resolved by gated-trapped ion mobility spectrometry (gated-TIMS) with negligible sulfo losses. Subsequent negative electron transfer dissociation (NETD) tandem mass spectrometry (MS/MS) analysis of TIMS-separated Hep/HS isomers generated extensive glycosidic and cross-ring fragments for confident isomer differentiation and structure elucidation. The high mobility resolution and preservation of labile sulfo modifications afforded by gated-TIMS MS analysis also allowed relative quantification of highly sulfated heparin isomers. These results show that the gated-TIMS-NETD MS/MS approach is useful for both qualitative and quantitative analysis of highly sulfated Hep/HS compounds in a manner not possible with other techniques.

Electron-ion reaction-based dissociation: A powerful ion activation method for the elucidation of natural product structures

The structural elucidation of natural products (NPs) remains a challenge due to their structurally diversities and unpredictable functionalities, motifs, and scaffolds. Tandem mass spectrometry (MS/MS) is an effective method that assists the full elucidation of complicated NP structures. Ion activation methods play a key role in determining the fragmentation pathways and the structural information obtained from MS/MS. Electron-ion reaction-based dissociation (ExD) methods, including electron capture dissociation (ECD), electron transfer dissociation (ETD), electron-induced dissociation (EID), and electron detachment dissociation (EDD), can induce the breakage of specific chemical bonds and the generation of distinct fragment ions. This review article provides an overview of the mechanisms, instrumentation, and typical applications related to ExD MS/MS in the structural elucidation of NPs, primarly including lipids, oligosaccharides, glycoconjugates, metabolites, and pharmaceutical drugs. This work aims to reveal the capacity and potential of ExD mass spectrometry in analyzing NPs and consequently helping the NP communities to utilize the modern capabilities of MS/MS in the discovery and evaluation of novel NPs.

Glycosaminoglycans analysis in blood and urine of patients with mucopolysaccharidosis

To explore the correlation between glycosaminoglycan (GAG) levels and mucopolysaccharidosis (MPS) type, we have evaluated the GAG levels in blood of MPS II, III, IVA, and IVB and urine of MPS IVA, IVB, and VI by tandem mass spectrometry. Dermatan sulfate (DS), heparan sulfate (HS), keratan sulfate (KS; mono-sulfated KS, di-sulfated KS), and the ratio of di-sulfated KS in total KS were measured. Patients with untreated MPS II had higher levels of DS and HS in blood while untreated MPS III had higher levels of HS in blood than age-matched controls. Untreated MPS IVA had higher levels of KS in blood and urine than age-matched controls. The ratio of blood di-sulfated KS/total KS in untreated MPS IVA was constant and higher than that in controls for children up to 10 years of age. The ratio of urine di-sulfated KS/total KS in untreated MPS IVA was also higher than that in age-matched controls, but the ratio in untreated MPS IVB was lower than controls. ERT reduced blood DS and HS in MPS II, and urine KS in MPS IVA patients, although GAGs levels remained higher than the observed in age-matched controls. ERT did not change blood KS levels in MPS IVA. MPS VI under ERT still had an elevation of urine DS level compared to age-matched controls. There was a positive correlation between blood and urine KS in untreated MPS IVA patients but not in MPS IVA patients treated with ERT. Blood and urine KS levels were secondarily elevated in MPS II and VI, respectively. Overall, measurement of GAG levels in blood and urine is useful for diagnosis of MPS, while urine KS is not a useful biomarker for monitoring therapeutic efficacy in MPS IVA.

Lasers and ion mobility: new additions to the glycosaminoglycanomics toolkit

Glycosaminoglycans are biopolymers present in mammalian cells or in the extracellular matrix. To address their structure, the nature of the hexuronic acids and the position of sulfate groups must be determined. Tandem mass spectrometry using collision induced dissociation or electron-based fragmentation techniques, is a well-established approach for the identification of glycans but suffers from the frequent lack of diagnostic fragments in the case of glycosaminoglycans. This review presents alternative fragmentation techniques, namely photofragmentation in the IR and the UV ranges. Alternative approaches based on the direct analysis of the molecular structure, including ion mobility spectrometry and ion spectroscopies are reviewed. The potential of future multidimensional workflows for glycosaminoglycanomics is discussed.

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry

The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. Graphical Abstract.

Heparin/heparan sulfate analysis by covalently modified reverse polarity capillary zone electrophoresis-mass spectrometry

Reverse polarity capillary zone electrophoresis coupled to negative ion mode mass spectrometry (CZE-MS) is shown to be an effective and sensitive tool for the analysis of glycosaminoglycan mixtures. Covalent modification of the inner wall of the separation capillary with neutral or cationic reagents produces a stable and durable surface that provides reproducible separations. By combining CZE-MS with a cation-coated capillary and a sheath flow interface, a rapid and reliable method has been developed for the analysis of sulfated oligosaccharides from dp4 to dp12. Several different mixtures have been separated and detected by mass spectrometry. The mixtures were selected to test the capability of this approach to resolve subtle differences in structure, such as sulfation position and epimeric variation of the uronic acid. The system was applied to a complex mixture of heparin/heparan sulfate oligosaccharides varying in chain length from dp3 to dp12 and more than 80 molecular compositions were identified by accurate mass measurement.

Increasing Analytical Separation and Duty Cycle with Nonlinear Analytical Mobility Scan Functions in TIMS-FT-ICR MS

In this work, nonlinear, stepping analytical mobility scan functions are implemented to increase the analytical separation and duty cycle during tandem Trapped Ion Mobility Spectrometry and FT-ICR MS operation. The differences between linear and stepping scan functions are described based on length of analysis, mobility scan rate, signal-to-noise, and mobility resolving power. Results showed that for the linear mobility scan function only a small fraction of the scan is sampled, resulting in the lowest duty cycle 0.5% and longest experiment times. Implementing nonlinear targeted scan functions for analysis of known mobilities resulted in increased duty cycle (0.85%) and resolving powers (R up to 300) with a 6-fold reduction in time from 30 to 5 min. For broad range characterization, a nonlinear mobility stepping scan function provided the best sensitivity, resolving power, duty cycle (4%), and points per peak. The applicability of nonlinear mobility scan functions for the analysis of complex mixtures is illustrated for the case of a direct infusion of a MCF-7 breast cancer cell digest, where isobaric peptides (e.g., DFTPAELR and TTILQSTGK) were separated in the mobility domain (R_IMS: 110) and identified based on their CCS, accurate mass (R_MS: 550k), and tandem MS using IRMPD in the ICR cell.

Isomer separation and effect of the degree of polymerization on the gas-phase structure of chondroitin sulfate oligosaccharides analyzed by ion mobility and tandem mass spectrometry

RATIONALE

Chondroitin sulfate (CS) glycosaminoglycans are bioactive sulfated polysaccharides comprising repeating units of uronic acid and N-acetyl galactose sulfated at various positions. The optimal length and sulfation pattern of the CS bioactive sequences remain elusive so that structure-activity relationships cannot be easily established. Development of efficient analytical methods allowing the differentiation of the various sulfation patterns of CS sequences is therefore of particular importance to correlate their biological functions to the sulfation pattern.

METHODS

Discrimination of different oligomers (dp2 to dp6) of synthetic chondroitin sulfate isomers was evaluated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative-ion mode from deprotonated and alkali adduct species. In addition, ion mobility mass spectrometry (IMS-MS) was used to study the influence of both the degree of polymerization and sulfate group location on the gas-phase conformation of CS oligomers.

RESULTS

ESI-MS/MS spectra of chondroitin sulfate isomers show characteristic product ions exclusively from alkali adduct species (Li, Na, K and Cs). Whatever the alkali adducts studied, MS/MS of chondroitin oligosaccharides sulfated at position 6 yields a specific product ion at m/z 139 while CS oligosaccharides sulfated at position 4 show a specific product ion at m/z 154. Being observed for the different CS oligomers di-, tetra- and hexasaccharides, these fragment ions are considered as diagnostic ions for chondroitin 6-O-sulfate and chondroitin 4-O-sulfate, respectively. IMS-MS experiments reveal that collision cross-sections (CCS) of CS oligomers with low charge states evolved linearly with degrees of polymerization indicating a similar gas-phase conformation.

CONCLUSIONS

This study allows the fast and unambiguous differentiation of CS isomers sulfated at position 6 or 4 for both saturated and unsaturated analogues from MS/MS experiments. In addition, the CCS linear evolution of CS oligomers in function of the degree of polymerization indicates that no folding occurs even for hexasaccharides.

Single Stage Tandem Mass Spectrometry Assignment of the C-5 Uronic Acid Stereochemistry in Heparan Sulfate Tetrasaccharides using Electron Detachment Dissociation

The analysis of heparan sulfate (HS) glycosaminoglycans presents many challenges, due to the high degree of structural heterogeneity arising from their non-template biosynthesis. Complete structural elucidation of glycosaminoglycans necessitates the unambiguous assignments of sulfo modifications and the C-5 uronic acid stereochemistry. Efforts to develop tandem mass spectrometric-based methods for the structural analysis of glycosaminoglycans have focused on the assignment of sulfo positions. The present work focuses on the assignment of the C-5 stereochemistry of the uronic acid that lies closest to the reducing end. Prior work with electron-based tandem mass spectrometry methods, specifically electron detachment dissociation (EDD), have shown great promise in providing stereo-specific product ions, such as the B3´ -CO2, which has been found to distinguish glucuronic acid (GlcA) from iduronic acid (IdoA) in some HS tetrasaccharides. The previously observed diagnostic ions are generally not observed with 2-O-sulfo uronic acids or for more highly sulfated heparan sulfate tetrasaccharides. A recent study using electron detachment dissociation and principal component analysis revealed a series of ions that correlate with GlcA versus IdoA for a set of 2-O-sulfo HS tetrasaccharide standards. The present work comprehensively investigates the efficacy of these ions for assigning the C-5 stereochemistry of the reducing end uronic acid in 33 HS tetrasaccharides. A diagnostic ratio can be computed from the sum of the ions that correlate to GlcA to those that correlate to IdoA. Graphical Abstract ᅟ.

Analysis of Photoirradiated Water Accommodated Fractions of Crude Oils Using Tandem TIMS and FT-ICR MS

For the first time, trapped ion mobility spectrometry (TIMS) in tandem with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is applied to the analysis of the low energy water accommodated fraction (WAF) of a crude oil as a function of the exposure to light. The TIMS-FT-ICR MS analysis provided, in addition to the heteroatom series identification, new insights into the WAF isomeric complexity (e.g., [m/z; chemical formula; collision cross section] data sets) for a better evaluation of the degree of chemical and structural photoinduced transformations. Inspection of the [m/z; chemical formula; collision cross section] data sets shows that the WAF composition changes as a function of the exposure to light in the first 115 h by initial photosolubilization of HC components and their photo-oxidation up to O_4-5 of mainly high double bond equivalence species (DBE > 9). The addition of high resolution TIMS (resolving power of 90-220) to ultrahigh resolution FT-ICR MS (resolving power over 400k) permitted the identification of a larger number of molecular components in a single analysis (e.g., over 47k using TIMS-MS compared to 12k by MS alone), with instances of over 6-fold increase in the number of molecular features per nominal mass due to the WAF isomeric complexity. This work represents a stepping stone toward a better understanding of the WAF components and highlights the need for better experimental and theoretical approaches to characterize the WAF structural diversity.

Recent innovations in the structural analysis of heparin

Heparin, the widely used anticoagulant drug, is unusual among major pharmaceutical agents being neither single chemical entity nor a defined mixture of compounds. Its composition, while conforming to approximate average disaccharide composition or sulfation levels, exhibits heterogeneity and variability depending on the source, as well as its geographical origin. Furthermore, individual polysaccharide chains, whose physico-chemical properties are extremely similar, cannot be separated with current state-of-the-art techniques, presenting a challenge to those interested in the quality control of heparin, in ensuring its provenance and safety, and those with an interest in investigating the relationships between its structure and biological activity. The review consists of two main sections: The first is the Introduction, comprising (i) The History, Occurrence and Use of Heparin and (ii) Approaches to Structure-Activity Relationships. The second section is Improved Techniques for Structural Analysis, comprising; (i) Separation and Identification, (ii) Spectroscopic Methods, (iii) Enzymatic Approaches and (iv) Other Physico-Chemical Approaches. The ~60 references cover recent technological advances in the study of heparin structural analysis, largely since 2010.

IRMPD Spectroscopy Sheds New (Infrared) Light on the Sulfate Pattern of Carbohydrates

IR spectroscopy of gas-phase ions is proposed to resolve positional isomers of sulfated carbohydrates. Mass spectrometric fingerprints and gas-phase vibrational spectra in the near and mid-IR regions were obtained for sulfated monosaccharides, yielding unambiguous signatures of sulfated isomers. We report the first systematic exploration of the biologically relevant but notoriously challenging deprotonated state in the near IR region. Remarkably, anions displayed very atypical vibrational profiles, which challenge the well-established DFT (Density Functionnal Theory) modeling. The proposed approach was used to elucidate the sulfate patterns in glycosaminoglycans, a ubiquitous class of mammalian carbohydrates, which is regarded as a major challenge in carbohydrate structural analysis. Isomeric glycosaminoglycan disaccharides from heparin and chondroitin sources were resolved, highlighting the potential of infrared multiple photon dissociation spectroscopy as a novel structural tool for carbohydrates.

Glycosaminoglycans detection methods: Applications of mass spectrometry

Glycosaminoglycans (GAGs) are long blocks of negatively charged polysaccharides. They are one of the major components of the extracellular matrix and play multiple roles in different tissues and organs. The accumulation of undegraded GAGs causes mucopolysaccharidoses (MPS). GAGs are associated with other pathological conditions such as osteoarthritis, inflammation, diabetes mellitus, spinal cord injury, and cancer. The need for further understanding of GAG functions and mechanisms of action boosted the development of qualitative and quantitative (alcian blue, toluidine blue, paper and thin layer chromatography, gas chromatography, high pressure liquid chromatography, capillary electrophoresis, 1,9-dimethylmethylene blue, enzyme linked-immunosorbent assay, mass spectrometry) techniques. The availability of quantitative techniques has facilitated translational research on GAGs into the medical field for: 1) diagnosis, monitoring, and screening for MPS; 2) analysis of GAG synthetic and degradation pathways; and 3) determination of physiological and pathological roles of GAGs. This review provides a history of development of GAG assays and insights about the use of tandem mass spectrometry and its applications for GAG analysis.

Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization

The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting. Graphical Abstract ᅟ.

Differential mobility spectrometry/mass spectrometry history, theory, design optimization, simulations, and applications

This review of differential mobility spectrometry focuses primarily on mass spectrometry coupling, starting with the history of the development of this technique in the Soviet Union. Fundamental principles of the separation process are covered, in addition to efforts related to design optimization and advancements in computer simulations. The flexibility of differential mobility spectrometry design features is explored in detail, particularly with regards to separation capability, speed, and ion transmission. 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:687-737, 2016.

De Novo Sequencing of Complex Mixtures of Heparan Sulfate Oligosaccharides

Here, we describe the first sequencing method of a complex mixture of heparan sulfate tetrasaccharides by LC-MS/MS. Heparin and heparan sulfate (HS) are linear polysaccharides that are modified in a complex manner by N- and O-sulfation, N-acetylation, and epimerization of the uronic acid. Heparin and HS are involved in various essential cellular communication processes. The structural analysis of these glycosaminoglycans is challenging due to the lability of their sulfate groups, the high heterogeneity of modifications, and the epimerization of the uronic acids. While advances in liquid chromatography (LC) and mass spectrometry (MS) have enabled compositional profiling of HS oligosaccharide mixtures, online separation and detailed structural analysis of isomeric and epimeric HS mixtures has not been achieved. Here, we report the development and evaluation of a chemical derivatization and tandem mass spectrometry method that can separate and identify isomeric and epimeric structures from complex mixtures. A series of well-defined synthetic HS tetrasaccharides varying in sulfation patterns and uronic acid epimerization were analyzed by chemical derivatization and LC-MS/MS. These synthetic compounds made it possible to establish relationships between HS structure, chromatographic behavior and MS/MS fragmentation characteristics. Using the analytical characteristics determined through the analysis of the synthetic HS tetrasaccharide standards, an HS tetrasacharide mixture derived from natural sources was successfully sequenced. This method represents the first sequencing of complex mixtures of HS oligosaccharides, an essential milestone in the analysis of structure-function relationships of these carbohydrates.

Eradicating mass spectrometric glycan rearrangement by utilizing free radicals

We designed and synthesized a methylated free radical activated glycan sequencing reagent (Me-FRAGS) for eliminating mass spectrometric glycan rearrangement.

Mass spectrometric glycan rearrangement is problematic because it provides misleading structural information. Here we report on a new reagent, a methylated free radical activated glycan sequencing reagent (Me-FRAGS), which combines a free radical precursor with a methylated pyridine moiety that can be coupled to the reducing terminus of glycans. The collisional activation of Me-FRAGS-derivatized glycans generates a nascent free radical that concurrently induces abundant glycosidic bond and cross-ring cleavage without the need for subsequent activation. The product ions resulting from glycan rearrangement, including internal residue loss and multiple external residue losses, are precluded. Glycan structures can be easily assembled and visualized using a radical driven glycan deconstruction diagram (R-DECON diagram). The presence and location of N-acetylated saccharide units and branch sites can be identified from the characteristic dissociation patterns observed only at these locations. The mechanisms of dissociation are investigated and discussed. This Me-FRAGS based mass spectrometric approach creates a new blueprint for glycan structure analysis.

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.

Applications of capillary electrophoresis electrospray ionization mass spectrometry in glycosaminoglycan analysis

Proteoglycans (PGs) represent a class of heavily glycosylated proteins distributed in the extracellular matrix, connective tissues, and on the surface of many cell types where, as functional molecules, regulate important biological processes. Structurally, PGs consist of a core protein linked to glycosaminoglycan (GAG) chains, which basically determine the properties and activities of PGs. In view of the structural complexity of GAGs and the existing correlation between this structure and PG functions, systematic efforts are invested into development of analytical methods for GAG characterization. Although less popular and of higher technical difficulty than liquid-based chromatographic methods, CE coupled with ESI MS contributed lately an important progress to glycosaminoglycomics field. In this review article, the most significant CE ESI MS and MS/MS applications in GAG research are highlighted and critically assessed. The advantages and the limitations of each concept as well as the possible further methodological refinements are also concisely discussed. Finally, the review presents the perspectives of CE ESI MS in GAG analysis along with the objectives, which still need to be reached in the near future.