Monosaccharide Identification as a First Step toward de Novo Carbohydrate Sequencing: Mass Spectrometry Strategy for the Identification and Differentiation of Diastereomeric and Enantiomeric Pentose Isomers

Graph theoretical descriptors differentiate d-Mannose isomers in the principal component proposed feature space: A computational approach

The intricate nature of carbohydrates, particularly monosaccharides, stems from the existence of several chiral centers within their tertiary structures. Predicting and characterizing the molecular geometries and electrostatic landscapes of these substances is difficult due to their complex electrical properties. Moreover, these structures can display a substantial degree of conformational flexibility due to the presence of many rotatable bonds. Moreover, identifying and distinguishing between D and L enantiomers of monosaccharides presents a significant analytical obstacle since there is a need for empirically measurable properties that can distinguish them. This work uses Principal Component Analysis (PCA) to explore the chemical information included in 3D descriptors in order to comprehend the conformational space of d-Mannose stereoisomers. The isomers may be discriminated by utilizing 3D matrix-based indices, geometrical descriptors, and RDF descriptors. The isomers can be distinguished by descriptors, such as the Harary-like index from the reciprocal squared geometrical matrix (H_RG), Harary-like index from Coulomb matrix (H_Coulomb), Wiener-like index from Coulomb matrix (Wi_Coulomb), Wiener-like index from geometrical matrix (Wi_G), Graph energy from Coulomb matrix (SpAbs_Coulomb), Spectral absolute deviation from Coulomb matrix (SpAD_Coulomb), and Spectral positive sum from Coulomb matrix (SpPos_Coulomb). Among these descriptors, the first two, H_RG and H_Coulomb, perform the best in differentiation among the 3D-Matrix-Based Descriptors (3D-MBD) class. The results obtained from this study provide a significant chemical insight into the structural characteristics of the compounds inside the graph theoretical framework. These findings are likely to serve as the basis for developing new methods for analytical experiments.

Contemporary strategies and approaches for characterizing composition and enhancing biofilm penetration targeting bacterial extracellular polymeric substances

Extracellular polymeric substances (EPS) constitutes crucial elements within bacterial biofilms, facilitating accelerated antimicrobial resistance and conferring defense against the host's immune cells. Developing precise and effective antibiofilm approaches and strategies, tailored to the specific characteristics of EPS composition, can offer valuable insights for the creation of novel antimicrobial drugs. This, in turn, holds the potential to mitigate the alarming issue of bacterial drug resistance. Current analysis of EPS compositions relies heavily on colorimetric approaches with a significant bias, which is likely due to the selection of a standard compound and the cross-interference of various EPS compounds. Considering the pivotal role of EPS in biofilm functionality, it is imperative for EPS research to delve deeper into the analysis of intricate compositions, moving beyond the current focus on polymeric materials. This necessitates a shift from heavy reliance on colorimetric analytic methods to more comprehensive and nuanced analytical approaches. In this study, we have provided a comprehensive summary of existing analytical methods utilized in the characterization of EPS compositions. Additionally, novel strategies aimed at targeting EPS to enhance biofilm penetration were explored, with a specific focus on highlighting the limitations associated with colorimetric methods. Furthermore, we have outlined the challenges faced in identifying additional components of EPS and propose a prospective research plan to address these challenges. This review has the potential to guide future researchers in the search for novel compounds capable of suppressing EPS, thereby inhibiting biofilm formation. This insight opens up a new avenue for exploration within this research domain.

Enterohaemorrhagic E. coli utilizes host- and microbiota-derived L-malate as a signaling molecule for intestinal colonization

The mammalian gastrointestinal tract is a complex environment that hosts a diverse microbial community. To establish infection, bacterial pathogens must be able to compete with the indigenous microbiota for nutrients, as well as sense the host environment and modulate the expression of genes essential for colonization and virulence. Here, we found that enterohemorrhagic Escherichia coli (EHEC) O157:H7 imports host- and microbiota-derived L-malate using the DcuABC transporters and converts these substrates into fumarate to fuel anaerobic fumarate respiration during infection, thereby promoting its colonization of the host intestine. Moreover, L-malate is important not only for nutrient metabolism but also as a signaling molecule that activates virulence gene expression in EHEC O157:H7. The complete virulence-regulating pathway was elucidated; the DcuS/DcuR two-component system senses high L-malate levels and transduces the signal to the master virulence regulator Ler, which in turn activates locus of enterocyte effacement (LEE) genes to promote EHEC O157:H7 adherence to epithelial cells of the large intestine. Disruption of this virulence-regulating pathway by deleting either dcuS or dcuR significantly reduced colonization by EHEC O157:H7 in the infant rabbit intestinal tract; therefore, targeting these genes and altering physiological aspects of the intestinal environment may offer alternatives for EHEC infection treatment.

An identification method to distinguish monomeric sugar isomers on glycopeptides

A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.

Exploration of chiral drugs as references for chiral discrimination of valsartan and voriconazole by tandem mass spectrometry

The use of mass spectrometry for chiral recognition and quantification has attracted great interest owing to its speed, sensitivity, specificity, and tolerance. However, searching for chiral selectors in chiral analyses using mass spectrometry is still problematic. In this study, chiral drugs could be applied as references for the chiral recognition and enantiomeric quantification of valsartan and voriconazole. Two novel pairs of metal-bound diastereomeric complex ions were detected by mass spectrometry, namely, nickel (II)-bound dimeric ions [NiII (2R,5S-emtricitabine) (S-valsartan)-H]+ and [NiII (2R,5S-emtricitabine) (R-valsartan)-H]+ and copper (II)-bound dimeric ions [CuII (S,S,S-enalaprilat) (2S,3R-voriconazole)-H]+ and [CuII (S,S,S-enalaprilat) (2R,3S-voriconazole)-H]+ . The resulting diastereomers were successfully identified based on the relative intensities of their characteristic fragments using tandem mass spectrometry. The logarithm of the characteristic fragment ion abundance ratio exhibited a good linear relationship with the enantiomeric excess. Density functional theory calculations were also performed to elucidate the mechanism of the structural differences observed in the MS results. This established approach proves that chiral drugs can serve as ligands for the rapid recognition and quantitative analysis of other chiral drugs without a chiral chromatographic column or complex sample pretreatment.

Chemical Sensors using Single-Molecule Electrical Measurements

Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.

Advances in single-molecule junctions as tools for chemical and biochemical analysis

The development of miniaturized electronics has led to the design and construction of powerful experimental platforms capable of measuring electronic properties to the level of single molecules, along with new theoretical concepts to aid in the interpretation of the data. A new area of activity is now emerging concerned with repurposing the tools of molecular electronics for applications in chemical and biological analysis. Single-molecule junction techniques, such as the scanning tunnelling microscope break junction and related single-molecule circuit approaches have a remarkable capacity to transduce chemical information from individual molecules, sampled in real time, to electrical signals. In this Review, we discuss single-molecule junction approaches as emerging analytical tools for the chemical and biological sciences. We demonstrate how these analytical techniques are being extended to systems capable of probing chemical reaction mechanisms. We also examine how molecular junctions enable the detection of RNA, DNA, and traces of proteins in solution with limits of detection at the zeptomole level.

Collision-induced dissociation of Na+-tagged ketohexoses: experimental and computational studies on fructose

Collision-induced dissociation tandem mass spectrometry (CID-MSⁿ) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na⁺-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), β-fructofuranose (βFruf), α-fructopyranose (αFrup), and β-fructopyranose (βFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSⁿ can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.

Multidimensional identification of disaccharide isomers based on non-covalent complexes and tandem mass spectrometry

Glycans are the most abundant organic polymers in nature. They are essential to living organisms and regulate a wide range of biological functions. However, mass spectrometry-based identification of glycan isomers remains challenging due to the complexity of their structures including their complex compositions, linkages, and anomeric configurations. In this study, two novel complex ions, the mononuclear copper-bound dimeric ions [(Cu²⁺)(A)(L-His)-H]⁺ and the mononuclear copper-bound quaternary ions [(Cu²⁺)(A)(L-Ser)₃-H]⁺ (where A denotes a disaccharide, and L-Ser/His denotes l-serine/histidine), were designed for the collision-induced dissociation-based identification and relative quantification of 14 disaccharide isomers. When the unique fragmentation patterns of the above two types of complex ions were mapped into a three-dimensional vector, all the isomers were completely distinguished. Of note, the established method is able to identify mixtures of linkage isomers only using tandem mass spectrometry based on linkage-specific fragment ions of histidine-based complex ions. Finally, the method was successfully applied to the identification and relative quantification of two disaccharide isomers (lactose and sucrose) in dairy beverages. In conclusion, the established method is sensitive to subtle structural differences in disaccharide isomers and has the potential to be used for the differentiation of various glycans.

Differentiation of disaccharide isomers via a combination of IR and UV photodissociation mass spectrometry

RATIONALE

The challenge of glycan identification due to their structural complexity and diversity has profited enormously from recent developments in mass spectrometry (MS)-related methods. For photodissociation MS, infrared (IR) and ultraviolet (UV) lasers can generate complementary fragment ions, so an effective combination of the two methods may provide rich and valuable fragmentation patterns for glycan analysis.

METHODS

A 7.0 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer equipped with a double-beam laser system was applied for the experiments. 3,5-Diiodo-L-tyrosine was selected as the assistant molecule to form complex ions with ten isomeric disaccharides through electrospray ionization. The complex ions were further isolated and irradiated by IR and UV lasers separately or continuously in the FTICR cell.

RESULTS

By combining the two complementary fragment spectra generated from the IR and UV lasers, a clear identification of all the ten isomers was achieved using their binary codes based on their fragmentation patterns. The double-beam method simplifies the experiment by introducing the two lasers sequentially in one experiment, providing richer fragmentation patterns and making the full discrimination easier.

CONCLUSIONS

This study demonstrates the capabilities of the combination of IR and UV photodissociation MS in the identification of diverse glycan isomers. The double-beam photodissociation method described here distinguished compositional, configurational and connectivity disaccharide isomers successfully. Compared with the data accumulation method based on separate IR and UV experiments, this method is simpler, faster, more flexible and also characterized by richer fragmentation patterns.

Comprehensive analysis of natural polysaccharides from TCMs: a generic approach based on UPLC-MS/MS

Here, we report a new application using liquid chromatography-electrospray mass spectrometry (UHPLC-ESI-MS) using aldononitrile acetate derivatives for simultaneous baseline separation and detection of eight neutral saccharides, two uronic acids, one ketose, and eight alditols within 14 min. The separation was performed on a Cortecs C₁₈ column using acetonitrile (A) and water (B) as the mobile phase with gradient elution. The target components were detected in selected ion monitoring (SIM) mode by mass spectrometry with an electrospray ionization (ESI) source operating in positive ionization mode. A comparison with traditional methods was used to determine the validity of the results. The UHPLC-ESI-MS method was used for quantitative analysis of free carbohydrates in water extracts of Crataegus pinnatifida as well as determination of Polygonatum cyrtonema and Glossy ganoderma monosaccharides in polysaccharides. The results demonstrate that this protocol is a comprehensive and effective technique for qualitative and quantitative analysis of plant polysaccharides from TCMs.

Non-derivatization strategy for the comprehensive characterization of neutral monosaccharide isomers and neutral disaccharide isomers using hydrophilic interaction liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry

Monosaccharide isomers and disaccharide isomers widely exist in nature, playing a key role in a number of important biological processes. However, due to high structural similarity and high polarity, the characterization of monosaccharide isomers, disaccharide isomers, as well as the analysis of monosaccharide composition of polysaccharides by a method that does not require derivatization is an ongoing challenge. Herein, we proposed a simple method for rapid discrimination of non-derivatized neutral monosaccharide, and disaccharide isomers using hydrophilic interaction liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry (HILIC-Q/TOF-MS). In this work, we optimized the experimental parameters, and detailed approaches to discriminate the precursor ions, deprotonated ions, and fragment ions are proposed, as well. To discriminate the various ions, the retention times, the relative abundance (RA) of precursor ions and fragment ions at different collision energies, the relative abundance ratio (RAR) of fragment ions to deprotonated ions or precursor ions were considered for characterization of neutral monosaccharide and disaccharide isomers. Finally, this strategy was successfully applied to analyzing the monosaccharide composition of neutral disaccharides, polysaccharides, and an aqueous extract of Moringa oleifera seeds. The experimental results revealed that the HILIC-Q/TOF-MS is an effective and convenient strategy for rapid differentiation of monosaccharide isomers and disaccharide isomers, which may serve as a general platform for the analysis of neutral polysaccharides, food, medicinal plants, and herbs.

Distinguishment of Glycan Isomers by Trapped Ion Mobility Spectrometry

The in-depth study of glycan has drawn large research interests since it is one of the main biopolymers on the earth with a variety of biological functions. However, the distinguishment of glycans is still difficult due to the similarity of the monosaccharide building block, the anomer, and the linkage of glycosidic bonds. In this study, four novel and representative copper-bound diastereoisomeric complex ions were simultaneously detected in a single measurement by trapped ion mobility mass spectrometry, including mononuclear copper-bound dimeric ions [(Cu²⁺)(A)(l-Ser)-H]⁺ and [(Cu²⁺)(A)(l-His)-H]⁺, the mononuclear copper-bound trimeric ion [(Cu²⁺)(A)(l-Ser)(l-His)-H]⁺, and the binuclear copper-bound tetrameric ion [(Cu²⁺)₂(A)(l-Ser)₂(l-His)-3H]⁺ (where A denotes an oligosaccharide, and l-Ser and l-His denote l-serine and l-histidine, respectively). By combining the collision cross sections of complex ions, 23 oligosaccharide isomers were successfully distinguished including two pairs of sialylated glycan linkage isomers. In addition, due to the unique dissociation pathways of the trimeric ion, both the relative and absolute quantification of the individual isomer in the mixture could be determined using a mass spectrometry-based kinetic method. Finally, the method established above was successfully applied to the identification and quantification of glycan isomers in dairy beverages and juice. The method in the present study was sensitive to the fine difference of glycan isomers and might have wide applicability in glycoscience.

Quantification of monosaccharide enantiomers using optical properties of hydrogen-bonded tryptophan

Chiral recognition between amino acids and monosaccharides in the gas phase was investigated as a model for chemical evolution in interstellar molecular clouds. Ultraviolet (UV) photodissociation spectra and product ion spectra of cold gas-phase hydrogen-bonded clusters of protonated tryptophan (Trp) and a pentose, including ribose and arabinose, were obtained using a tandem mass spectrometer equipped with an electrospray ionization source and a temperature-controlled ion trap. The relative intensity of the signal arising from the S₁-S₀ transition of protonated Trp observed at approximately 285 nm in the UV photodissociation spectrum of homochiral H⁺(d-Trp)(d-ribose) was significantly higher than that of heterochiral H⁺(l-Trp)(d-ribose), corresponding to the ππ* state of the Trp indole ring. Optical properties of Trp in the clusters induced by 285-nm photoexcitation were applied to the identification and quantification of pentose enantiomers in solution. Pentose enantiomeric excess in solution was determined from relative abundances observed in a single product ion spectrum of 285-nm photoexcited hydrogen-bonded clusters of H⁺(l-Trp) and pentose. A mixture of two pentoses could also be quantified by this method. The geometric and electronic structures of Trp enable recognition of biological molecules through hydrogen bonding.

Poly-Amido-Saccharides (PASs): Functional Synthetic Carbohydrate Polymers Inspired by Nature

Carbohydrates are ubiquitous in nature, playing vital roles in all organisms ranging from metabolism to intercellular signaling. Polysaccharides, repeating units of small molecule carbohydrates, are hydrophilic, densely functionalized, stereoregular, and rigid macromolecules, and these characteristics are simultaneously advantageous in biomedical applications while presenting major hurdles for synthetic methodology and development of structure property relationships. While naturally obtained polysaccharides are widely utilized in the biochemical and medical literature, their poor physicochemical definition and the potential for contaminated samples hinders the clinical translation of this work. To address the need for new methods to synthesize carbohydrate polymers, we reported a novel class of biomaterials (Poly-Amido-Saccharides; PAS) in 2012. PASs share many properties with natural polysaccharides, such as hydrophilicity, dense hydroxyl functionality, stereoregularity, and a rigid backbone. PASs are connected by an α-1,2-amide linkage, instead of an ether linkage, that confers resistance to enzymatic and hydrolytic degradation and leads to a unique helical conformation. Importantly, our synthetic methodology affords control over molecular weight distribution resulting in pure, well-defined polymers. This Account provides an overview of the development of PAS, from the factors that initially motivated our research to current efforts to translate functional PAS to biomedical applications. We detail the synthesis of glucose- and galactose-based PAS and their biophysical properties including conformation analysis, lectin interactions, cell internalization, and water solubility. Additionally, we describe postpolymerization modification strategies to afford PASs that act as protein stabilizers. We also highlight our recent efforts toward a mechanistic understanding of monomer synthesis via [2 + 2] cycloaddition reactions in order to develop novel monomers with different stereochemistry and amine or alkyl functionality, thereby accessing functional carbohydrate polymers. Throughout our work, we apply computational and theoretical analysis to explain how properties at the monomer level (e.g., stereochemistry, functionality) significantly impact polymer properties, helical conformation, and bioactivities. Collectively, the results from the theoretical, synthetic, and applied aspects of this research advance us toward our goal of utilizing PASs in key biomedical applications as alternatives to natural polysaccharides. The importance of carbohydrates in nature and the versatility of their functions continue to inspire our investigation of new monomers, polymers, and copolymers, leveraging the advantageous properties of PAS to develop potential therapies.

Exploration of disaccharide as reference towards chiral recognition by the kinetic method

RATIONALE

A potential use of disaccharides was found as reference compounds in the kinetic method for chiral recognition and enantiomeric quantification.

METHODS

The experimental procedure consists of three steps: (1) mixing a metal salt, an analyte and a disaccharide at a molar ratio of 1:2:2 with an analyte concentration of 20 μM; (2) introducing the mixture into an electrospray ionization (ESI) mass spectrometry source; (3) isolating the ion [M^II (ref*)₂ (A) - H]⁺ and subjecting it to dissociation. Then through the relative ratio of two product ions combined with the kinetic method, chiral recognition and enantiomeric quantification can be achieved.

RESULTS

The method was verified with good chiral recognition for ten chiral amino acids and three chiral drugs. Among the ten amino acids, Tyr was observed to show best chiral selectivity (R_chiral  = 1.62) and good linearity with the correlation coefficient R²  = 0.9991 for the quantitation of the enantiomeric excess (ee) of D-Tyr. Among the tested chiral drugs, naproxen showed best chiral selectivity with R_chiral  = 1.56 and good linearity with the correlation coefficient R²  = 0.9997 for the quantitation of the ee of R-naproxen.

CONCLUSIONS

This established approach proves that a disaccharide can serve as a reference compound for chiral recognition using the kinetic method.

Advancing Solutions to the Carbohydrate Sequencing Challenge

Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.

Development of a Post-Column Liquid Chromatographic Chiral Addition Method for the Separation and Resolution of Common Mammalian Monosaccharides

The first solely MS-based methodology for the identification and resolution of the ten common mammalian monosaccharides is presented. Based on Cooks' fixed ligand kinetic method, this technique is effective on multiple classes of monosaccharides and includes the first example of two fixed ligand combinations used in a single multiplexed experiment. Subsequently, a post-HPLC chiral addition method is used in conjunction with this newly developed MS methodology for the separation and identification of mixtures of common neutral mammalian monosaccharides. This proposed technique is able to overcome a limitation of present carbohydrate analysis methods, namely the simultaneous isomeric resolution of multiple monosaccharides in a mixture. Graphical Abstract.

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. Graphical Abstract ᅟ.

Ion mobility and gas phase H/D exchange: revealing the importance of a single hydrogen bond for the chiral recognition of crown ether ammonium complexes

Two new BINOL-based chiral crown ether/ammonium complexes are studied by travelling-wave ion-mobility spectrometry. Homo- and heterochiral crown ether/ammonium complexes differ in their collision cross sections, and these differences go along with changes in hydrogen bonding as revealed by gas phase H/D-exchange experiments. Applications for the determination of enantiomeric excess are discussed.

Scope and limitations of carbohydrate hydrolysis for de novo glycan sequencing using a hydrogen peroxide/metallopeptide-based glycosidase mimetic

Acidic hydrolysis is commonly used as a first step to break down oligo- and polysaccharides into monosaccharide units for structural analysis. While easy to set up and amenable to mass spectrometry detection, acid hydrolysis is not without its drawbacks. For example, ring-destruction side reactions and degradation products, along with difficulties in optimizing conditions from analyte to analyte, greatly limits its broad utility. Herein we report studies on a hydrogen peroxide/CuGGH metallopeptide-based glycosidase mimetic design for a more efficient and controllable carbohydrate hydrolysis. A library of methyl glycosides consisting of ten common monosaccharide substrates, along with oligosaccharide substrates, was screened with the artificial glycosidase for hydrolytic activity in a high-throughput format with a robotic liquid handling system. The artificial glycosidase was found to be active towards most screened linkages, including alpha- and beta-anomers, thus serving as a potential alternative method for traditional acidic hydrolysis approaches of oligosaccharides.

Chiral detection of entecavir stereoisomeric impurities through coordination with R-besivance and ZnII using mass spectrometry

In this study, a mass spectrometry (MS)-based kinetic method (KM) is shown to be successful at analyzing a multichiral center drug stereoisomer, entecavir (ETV), both qualitatively and quantitatively. On the basis of the KM, the bivalent complex ion [M^II (A)(ref*)₂ ]²⁺ (M^II  = divalent metal ion, A = analyte, and ref* = chiral reference) was set as precursor ion in MS/MS. The experiment results suggest strong chiral selectivity between ETV and its isomers when using Zn^II coordinated with the chiral reference R-besivance (R-B). The logarithm of the fragment ion abundance ratio and the enantiomeric percentage (%) exhibits a strong linear relation because of the competitive loss of the reference and analyte. The product ion pair [Zn^II (R-B)A-H]⁺ (m/z 733) and [Zn^II (R-B)₂ -H]⁺ (m/z 849), together with [R-B + H]⁺ (m/z 394) and [A + H]⁺ (m/z 278), can realize the identification of ETV and all of its chiral isomers. Theoretical calculation were also performed using the B3LYP functional with the 6-31G* and LanL2DZ basis set to clarify the mechanism of structural difference of these bivalent complex ions. The results reveal that MS-KM can be used to detect optical impurities without a chiral chromatographic column and fussy sample pretreatment. The established method has been used to determine stereoisomeric impurities of less than 0.1% in ETV crude drug, a demonstration of its simple and effective nature for rapid detection of stereoisomeric impurities.

A High-Throughput Mass-Spectrometry-Based Assay for Identifying the Biochemical Functions of Putative Glycosidases

The most commonly employed glycosidase assays rely on bulky ultraviolet or fluorescent tags at the anomeric position in potential carbohydrate substrates, thereby limiting the utility of these assays for broad substrate characterization. Here we report a qualitative mass spectrometry-based glycosidase assay amenable to high-throughput screening for the identification of the biochemical functions of putative glycosidases. The assay utilizes a library of methyl glycosides and is demonstrated on a high-throughput robotic liquid handling system for enzyme substrate screening. Identification of glycosidase biochemical function is achieved through the observation of an appropriate decrease in mass between a potential sugar substrate and its corresponding product by electrospray ionization mass spectrometry (ESI-MS). In addition to screening known glycosidases, the assay was demonstrated to characterize the biochemical function and enzyme substrate competency of the recombinantly expressed product of a putative glycosidase gene from the thermophilic bacterium Thermus thermophilus.

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.

Identifying the D-Pentoses Using Water Adduction to Lithium Cationized Molecule

A method has been developed that is capable of distinguishing an exhaustive list of underivatized D-pentoses with only a mass spectrometer. Electrospray ionization (ESI) of a solution containing a pentose and a lithium salt yields [Pentose + Li]⁺. These lithiated pentoses adduct water in a quadrupole ion trap. The reaction rate of water adduction is unique for several of the pentose isomers. Additionally, there are multiple potential gas-phase lithiation sites to form [Pentose + Li]⁺. A mixture of ions with at least one reactive (water adducting) and at least one unreactive (non-adducting) lithiation site is formed for each pentose. The water adduction reaction rate along with the unreactive fraction of lithiated pentose can be used to completely discriminate all D-pentoses. Graphical Abstract ᅟ.

Recent Liquid Chromatographic Approaches and Developments for the Separation and Purification of Carbohydrates

Carbohydate purification remains a bottleneck in securing analytical standards from natural sources or by chemical or enzymatic synthesis. This review highlights the scope and remaining limitations of recent approaches and methods development in liquid chromatography for robust and higher-throughput carbohydrate separation and isolation.

Bottom-Up Elucidation of Glycosidic Bond Stereochemistry

The lack of robust, high-throughput, and sensitive analytical strategies that can conclusively map the structure of glycans has significantly hampered progress in fundamental and applied aspects of glycoscience. Resolution of the anomeric α/β glycan linkage within oligosaccharides remains a particular challenge. Here, we show that "memory" of anomeric configuration is retained following gas-phase glycosidic bond fragmentation during tandem mass spectrometry (MS²). These findings allow for integration of MS² with ion mobility spectrometry (IM-MS²) and lead to a strategy to distinguish α- and β-linkages within natural underivatized carbohydrates. We have applied this fragment-based hyphenated MS technology to oligosaccharide standards and to de novo sequencing of purified plant metabolite glycoconjugates, showing that the anomeric signature is also observable in fragments derived from larger glycans. The discovery of the unexpected anomeric memory effect is further supported by IR-MS action spectroscopy and ab initio calculations. Quantum mechanical calculations provide candidate geometries for the distinct anomeric fragment ions, in turn shedding light on gas-phase dissociation mechanisms of glycosidic linkages.

Enantiomeric Excess Determination for Monosaccharides Using Chiral Transmission to Cold Gas-Phase Tryptophan in Ultraviolet Photodissociation

Chiral transmission between monosaccharides and amino acids via photodissociation in the gas phase was examined using a tandem mass spectrometer fitted with an electrospray ionization source and a cold ion trap in order to investigate the origin of the homochirality of biomolecules in molecular clouds. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of the monosaccharide enantiomers glucose (Glc) and galactose (Gal) with protonated L-tryptophan H⁺(L-Trp) were obtained by photoexcitation of the indole ring of L-Trp. L-Trp dissociated via C_α-C_β bond cleavage when noncovalently complexed with D-Glc; however, no dissociation of L-Trp occurred in the homochiral H⁺(L-Trp)(L-Glc) noncovalent complex, where the energy absorbed by L-Trp was released through the evaporation of L-Glc. This enantioselective photodissociation of Trp was due to the transmission of chirality from Glc to Trp via photodissociation in the gas-phase noncovalent complexes, and was applied to the quantitative chiral analysis of monosaccharides. The enantiomeric excess of monosaccharides in solution could be determined by measuring the relative abundance of the two product ions in a single photodissociation mass spectrum of the cold gas-phase noncovalent complex with H⁺(L-Trp), and by referring to the linear relationships derived in this work. Graphical Abstract ᅟ.

Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling

Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM–MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.

Carbohydrates are common biological molecules, but display huge stereochemical complexity that often cannot be elucidated by mass spectrometry. Here the authors show that recognition tunnelling can distinguish individual stereoisomers, utilizing picomole quantities of analytes.

PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications

Custom software entitled Plant Metabolite Annotation Toolbox (PlantMAT) has been developed to address the number one grand challenge in metabolomics, which is the large-scale and confident identification of metabolites. PlantMAT uses informed phytochemical knowledge for the prediction of plant natural products such as saponins and glycosylated flavonoids through combinatorial enumeration of aglycone, glycosyl, and acyl subunits. Many of the predicted structures have yet to be characterized and are absent from traditional chemical databases, but have a higher probability of being present in planta. PlantMAT allows users to operate an automated and streamlined workflow for metabolite annotation from a user-friendly interface within Microsoft Excel, a familiar, easily accessed program for chemists and biologists. The usefulness of PlantMAT is exemplified using ultrahigh-performance liquid chromatography-electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC-ESI-QTOF-MS/MS) metabolite profiling data of saponins and glycosylated flavonoids from the model legume Medicago truncatula. The results demonstrate PlantMAT substantially increases the chemical/metabolic space of traditional chemical databases. Ten of the PlantMAT-predicted identifications were validated and confirmed through the isolation of the compounds using ultrahigh-performance liquid chromatography-mass spectrometry-solid-phase extraction (UHPLC-MS-SPE) followed by de novo structural elucidation using 1D/2D nuclear magnetic resonance (NMR). It is further demonstrated that PlantMAT enables the dereplication of previously identified metabolites and is also a powerful tool for the discovery of structurally novel metabolites.

Isomeric complexity of glycosylation documented by MSn

Re-analysis of two breast cancer cell lines, MCF-7 and MDA-MB-231, has shown multiple isomeric structures exposed by sequential mass spectrometry, MS ⁿ . Several released glycan compositions were re-evaluated, which indicated variations in polylactosamine and fucosylation structures. Probable isomer numbers, when considering both stereo and structural entities, are significant and the varying types are mentioned. The structural isomers of linkage position are most frequently considered, while stereo isomers are usually assumed from biosynthetic data. Evaluation of any new sample should be cautious and merits careful attention to empirical data. While isomers are usually considered a chromatographic problem (e.g., LCMS, IMMS) and most frequently considered a separations problem, such results will always be challenged by identification and documentation. MSⁿ data provide a direct spatial solution that includes spectral data for characterization (mass and abundance) supported by a universal library match feature.

Protocol for the purification of protected carbohydrates: toward coupling automated synthesis to alternate-pump recycling high-performance liquid chromatography

Given recent advances in automated oligosaccharide synthesis, analytical techniques that can be coupled to a synthetic framework are needed to not just identify but also purify to homogeneity protected carbohydrate compounds at levels of ≥99.5% purity. Herein, an alternate-pump recycling high-performance liquid chromatography (R-HPLC) method has been developed to allow purification of protected carbohydrates at levels of ≥99.5% purity.

Multidimensional Analysis of 16 Glucose Isomers by Ion Mobility Spectrometry

Diastereomeric adducts comprising an enantiomerically pure monosaccharide analyte, a peptide, and/or an amino acid and a divalent metal ion (for 16 different monosaccharide isomers) are generated by electrospray ionization and analyzed by combined ion mobility spectrometry-mass spectrometry (IMS-MS) techniques. Mobility distributions of [l-Ser + M + H](+) (where l-Ser is l-serine and M is a given monosaccharide), [l-Phe-Gly + M + H](+) (where l-Phe-Gly is l-phenylalanine-glycine), and [Mn(II) + (l-Phe-Gly - H) + M](+) complex ions are used to determine collision cross sections (ccs in Å(2)), and groups of cross sections for different clusters are proposed as means of identifying the sugar isomers. Within one type of complex, variations in ccs do not always allow delineation between the 16 glucose isomers, but interestingly, when ccs of three different ions are combined as a spatial vector, enantiomers are partially resolved. As a result of this analysis, l-glucose, d-glucose, l-allose, d-allose, d-gulose, d-galactose, and l-mannose are delineated, and for all eight enantiomeric pairs, d and l entities display different coordinates. In addition, different combinations of amino acids, peptide, and metal ions are surveyed, and the potential for yielding unique coordinates for the generated diastereomeric complexes is assessed.