High-sensitivity analytical approaches for the structural characterization of glycoproteins

[Recent advances of molecular imprinting technology for the separation and recognition of complex biological sample systems]

Given continuous improvements in industrial production and living standards, the analysis and detection of complex biological sample systems has become increasingly important. Common complex biological samples include blood, serum, saliva, and urine. At present, the main methods used to separate and recognize target analytes in complex biological systems are electrophoresis, spectroscopy, and chromatography. However, because biological samples consist of complex components, they suffer from the matrix effect, which seriously affects the accuracy, sensitivity, and reliability of the selected separation analysis technique. In addition to the matrix effect, the detection of trace components is challenging because the content of the analyte in the sample is usually very low. Moreover, reasonable strategies for sample enrichment and signal amplification for easy analysis are lacking. In response to the various issues described above, researchers have focused their attention on immuno-affinity technology with the aim of achieving efficient sample separation based on the specific recognition effect between antigens and antibodies. Following a long period of development, this technology is now widely used in fields such as disease diagnosis, bioimaging, food testing, and recombinant protein purification. Common immuno-affinity technologies include solid-phase extraction (SPE) magnetic beads, affinity chromatography columns, and enzyme linked immunosorbent assay (ELISA) kits. Immuno-affinity techniques can successfully reduce or eliminate the matrix effect; however, their applications are limited by a number of disadvantages, such as high costs, tedious fabrication procedures, harsh operating conditions, and ligand leakage. Thus, developing an effective and reliable method that can address the matrix effect remains a challenging endeavor. Similar to the interactions between antigens and antibodies as well as enzymes and substrates, biomimetic molecularly imprinted polymers (MIPs) exhibit high specificity and affinity. Furthermore, compared with many other biomacromolecules such as antigens and aptamers, MIPs demonstrate higher stability, lower cost, and easier fabrication strategies, all of which are advantageous to their application. Therefore, molecular imprinting technology (MIT) is frequently used in SPE, chromatographic separation, and many other fields. With the development of MIT, researchers have engineered different types of imprinting strategies that can specifically extract the target analyte in complex biological samples while simultaneously avoiding the matrix effect. Some traditional separation technologies based on MIP technology have also been studied in depth; the most common of these technologies include stationary phases used for chromatography and adsorbents for SPE. Analytical methods that combine MIT with highly sensitive detection technologies have received wide interest in fields such as disease diagnosis and bioimaging. In this review, we highlight the new MIP strategies developed in recent years, and describe the applications of MIT-based separation analysis methods in fields including chromatographic separation, SPE, diagnosis, bioimaging, and proteomics. The drawbacks of these techniques as well as their future development prospects are also discussed.

Functional Interface for Glycoprotein Sensing: Focusing on Biosensors

Glycosylated proteins or glycoproteins make up a large family of glycoconjugates, and they participate in a variety of fundamental biological events. Glycoproteins have become important biomarkers in the diagnosis and treatment of a number of tumors. Biosensors are quite suitable for glycoprotein detection. The design and fabrication of a functional sensing interface play a crucial role in the biosensor construction to target glycoproteins. The functional interface, particularly receptors, typically determines the key characteristics of a biosensor, such as selectivity and sensitivity. Antibody, peptide, aptamer, boronic acid derivative, lectin, and molecularly imprinted polymer are all capable receptors for glycoprotein recognition, and each of these will be discussed. Most glycoproteins exist in low abundance, thus rendering signal amplification techniques indispensable. Nucleic acid-mediated and nanomaterial-mediated signal amplification for the detection of glycoproteins will be focused on herein. This review aims to highlight these different functional interfaces for glycoprotein sensing.

Integrated analysis of natural glycans using a versatile pyrazolone-type heterobifunctional tag ANPMP

Glycans mediate various biological processes through carbohydrate-protein interactions, and glycan microarrays have become indispensable tools for understanding these mechanisms. However, advances in functional glycomics are hindered by the absence of convenient and universal methods for obtaining natural glycan libraries with diverse structures from glycoconjugates. To address this challenge, we have developed an integrative approach that enables one-pot release and simultaneously capture, separation, structural characterization, and functional analysis of N/O-glycans. Using this approach, glycoconjugates are incubated with a pyrazolone-type heterobifunctional tag-ANPMP to obtain glycan-2ANPMP conjugates, which are then converted to glycan-AEPMP conjugates. We prepared a tagged glycan library from porcine gastric mucin, soy protein, human milk oligosaccharides, etc. Following derivatization by N-acetylation and permethylation, glycans were subjected to detailed structural characterization by ESI-MSn analysis, which revealed >83 highly pure glycan-AEPMPs containing various natural glycan epitopes. A shotgun microarray is constructed to study the fine details of glycan-bindings by proteins and antisera.

Interdigitated impedimetric-based Maackia amurensis lectin biosensor for prostate cancer biomarker

Highly specific detection of tumor-associated biomarkers remains a challenge in the diagnosis of prostate cancer. In this research, Maackia amurensis (MAA) was used as a recognition element in the functionalization of an electrochemical impedance-spectroscopy biosensor without a label to identify cancer-associated aberrant glycosylation prostate-specific antigen (PSA). The lectin was immobilized on gold-interdigitated microelectrodes. Furthermore, the biosensor's impedance response was used to assess the establishment of a complex binding between MAA and PSA-containing glycans. With a small sample volume, the functionalized interdigitated impedimetric-based (IIB) biosensor exhibited high sensitivity, rapid response, and repeatability. PSA glycoprotein detection was performed by measuring electron transfer resistance values within a concentration range 0.01-100 ng/mL, with a detection limit of 3.574 pg/mL. In this study, the ability of MAA to preferentially recognize α2,3-linked sialic acid in serum PSA was proven, suggesting a potential platform for the development of lectin-based, miniaturized, and cost effective IIB biosensors for future disease detection.

Comprehensive Comparison of Bioactive N-Glycans among Seven Species of Livestock and Poultry Plasma Using a Relative Quantification Strategy

Glycans have been proven to play special roles in keeping human health as a class of nutritional and bioactive ingredients in many food materials. However, their broad use in the food industry is hindered by the lack of comprehensive analytical methods for high-quality food glycomics studies and large-quantity raw materials for their production. This study focuses on structural identification and quantitative comparison of bioactive N-glycans in seven species of livestock and poultry plasma as potential natural glycan resources by a novel comprehensive relative quantification strategy based on stable isotope labeling with nondeuterated and deuterated 4-methyl-1-(2-hydrazino-2-oxoethyl)-pyridinium bromide (d0/d7-HMP) in combination with linkage-specific derivatization of sialic acid residues. Methodological validation of the method in terms of detection sensitivity, signal resolution, quantification linearity, precision, and accuracy on model neutral and complicated sialylated glycans demonstrated its advantages over the existing methods. Based on this method, a series of bioactive N-glycans were found in seven species of livestock and poultry plasma, and their differences in structure, abundance percentages, and relative contents of N-glycans were revealed, demonstrating their excellent applicability for comprehensive food glycomics analysis and great exploitation potential of these plasma samples as large-quantity raw materials in producing bioactive N-glycans for application in food and pharmaceutical industries.

Electrochemical detection of glycoproteins using boronic acid-modified metal-organic frameworks as dual-functional signal reporters

The sensitive analysis of glycoproteins is of great importance for early diagnosis and prognosis of diseases. In this work, a sandwich-type electrochemical aptasensor was developed for the detection of glycoproteins using 4-formylphenylboric acid (FPBA)-modified Cu-based metal-organic frameworks (FPBA-Cu-MOFs) as dual-functional signal probes. The target captured by the aptamer-modified electrode allowed the attachment of FPBA-Cu-MOFs based on the interaction between boronic acid and glycan on glycoproteins. Large numbers of Cu2+ ions in FPBA-Cu-MOFs produced an amplified signal for the direct voltammetric detection of glycoproteins. The electrochemical aptasensor showed a detection limit as low as 6.5 pg mL-1 for prostate specific antigen detection. The method obviates the use of antibody and enzymes for molecular recognition and signal output. The dual-functional MOFs can be extended to the design of other biosensors for the determination of diol-containing biomolecules in clinical diagnosis.

Assessing the hydrophobicity of glycopeptides using reversed-phase liquid chromatography and tandem mass spectrometry

Retention time is one of the most important parameters that has been widely used to demonstrate the separation results obtained from liquid chromatography (LC) platforms. However, retention time can shift when samples are tested with different instruments and laboratories, which hinders the identification process of analytes when comparing data collected from different LC systems. To address this problem, hydrophobicity index was introduced for retention time normalization of the glycopeptides separated by reversed-phase LC (RPLC). Tandem MS was used for the detection and identification of glycopeptides. In addition, the influence of different types of glycans on the hydrophobicity of peptide backbones was studied by comparing the retention time of glycopeptides with their non-glycosylated counterparts. The hydrophobicity of tryptic digested glycopeptides derived from model glycoproteins, including bovine fetuin, α1-acid glycoprotein, and haptoglobin from human plasma, were evaluated based on the hydrophobicity index of the standard peptides from a peptide retention time calibration mixture. The reduction of hydrophobicity of multiple peptide backbones was observed due to the hydrophilic glycan structures. By comparing the hydrophobicity index of glycopeptides collected from different time and instruments, the day-to-day and lab-to-lab comparisons suggested high reliability and reproducibility of this approach. The RSD% of hydrophobicity index from inter-lab experiments was 1.2%, while the RSD% of retention time was 5.1%. Then, the applications of this method were demonstrated on complex glycopeptide samples extracted from human blood serum. The hydrophobicity index can be applied to address the retention time shift when using different instruments, thereby boosting confidence of the characterization of glycopeptides.

An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics

The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.

Linking aberrant glycosylation of plasma glycoproteins with progression of myelodysplastic syndromes: a study based on plasmonic biosensor and lectin array

Aberrant glycosylation of glycoproteins has been linked with various pathologies. Therefore, understanding the relationship between aberrant glycosylation patterns and the onset and progression of the disease is an important research goal that may provide insights into cancer diagnosis and new therapy development. In this study, we use a surface plasmon resonance imaging biosensor and a lectin array to investigate aberrant glycosylation patterns associated with oncohematological disease-myelodysplastic syndromes (MDS). In particular, we detected the interaction between the lectins and glycoproteins present in the blood plasma of patients (three MDS subgroups with different risks of progression to acute myeloid leukemia (AML) and AML patients) and healthy controls. The interaction with lectins from Aleuria aurantia (AAL) and Erythrina cristagalli was more pronounced for plasma samples of the MDS and AML patients, and there was a significant difference between the sensor response to the interaction of AAL with blood plasma from low and medium-risk MDS patients and healthy controls. Our data also suggest that progression from MDS to AML is accompanied by sialylation of glycoproteins and increased levels of truncated O-glycans and that the number of lectins that allow discriminating different stages of disease increases as the disease progresses.

Collision energies: Optimization strategies for bottom-up proteomics

Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.

Human milk whey glycoprotein N-glycans varied greatly among different maternal secretor status

Human milk glycans are complex carbohydrates, which play a pivotal role in infant health and neonatal development. Maternal secretor status is known to affect free oligosaccharides in milk. Here, the milk N-glycome of secretor (Se+) and nonsecretor (Se-) individuals was qualitatively and quantitatively analyzed by hydrophilic interaction chromatography-electrospray ionization-tandem mass spectrometry. The total glycosylation, fucosylation, and sialylation of N-glycans was three times higher in the Se+ group compared to the Se- group (p < 0.001) per equal volume of milk. Importantly, 52 out of 63 N-glycans-including the eight most abundant ones-differed greatly between Se+ and Se- individuals (p < 0.05). Moreover, nine N-glycans (H5N3F1, H6N3, H3N5F1, H5N5F1, H5N5F1S1, H5N4F3S1, H6N4F2S1, H6N5F4S1, and H8N7S1) were >10 times more abundant in Se+ milk than in Se- milk. These findings lay a glycomics-basis for designing personalized nutrition supplements for infants.

Site-specific, covalent immobilization of PNGase F on magnetic particles mediated by microbial transglutaminase

In the workflow of global N-glycosylation analysis, endoglycosidase-mediated removal of glycans from glycoproteins is an essential and rate-limiting step. Peptide-N-glycosidase F (PNGase F) is the most appropriate and efficient endoglycosidase for the removal of N-glycans from glycoproteins prior to analysis. Due to the high demand for PNGase F in both basic and industrial research, convenient and efficient methods are urgently needed to generate PNGase F, preferably in the immobilized form to solid phases. However, there is no integrated approach to implement both efficient expression, and site-specific immobilization of PNGase F. Herein, efficient production of PNGase F with a glutamine tag in Escherichia coli and site-specific covalent immobilization of PNGase F with this special tag via microbial transglutaminase (MTG) is described. PNGase F was fused with a glutamine tag to facilitate the co-expression of proteins in the supernatant. The glutamine tag was covalently and site-specifically transformed to primary amine-containing magnetic particles, mediated by MTG, to immobilize PNGase F. Immobilized PNGase F could deglycosylate substrates with identical enzymatic performance to that of the soluble counterpart, and exhibit good reusability and thermal stability. Moreover, the immobilized PNGase F could also be applied to clinical samples, including serum and saliva.

Novel Method for Adulterated Identification of Saneen Goat Milk Based on Free Oligosaccharides α3'-Galactosyllactose and N-Acetylhexaminyllactose as Marker Molecules

Methods for the detection of adulterated milk are essential for assessing the quality of goat milk products. We hypothesized that goat milk oligosaccharides could provide a basis for this purpose and compared the levels of α3'-galactosyllactose (α3'-GL) and N-acetylhexaminyllactose (NHL) between goat milk and bovine milk oligosaccharides using reverse-phase high-performance liquid chromatography. The α3'-GL was detected to be three times more abundant in goat milk than in bovine milk, whereas NHL showed the opposite trend. Linear relationships were established between the relative proportions of α3'-GL and NHL levels for different ratios of bovine and goat milk, with a minimum detection limit of 2% bovine milk. The new method was validated by analyses of adulterants in eight commercially available goat dairy products. Overall, the degree of adulteration in goat milk products can be determined based on the relative proportions of α3'-GL and NHL.

Profiling Serum Intact N-Glycopeptides Using Data-Independent Acquisition Mass Spectrometry

Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data-independent acquisition (DIA) mass spectrometry is an emerging technology with deep proteome coverage as well as accurate quantitative capability for large-scale proteomics studies and has also been applied to the field of glycoproteomics. In this protocol, we describe how to analyze data from a DIA experiment for profiling serum intact N-glycopeptides. We present a comprehensive data analysis workflow using GproDIA, including glycopeptide spectral library building, chromatographic feature extraction from the DIA data, and feature scoring with appropriate statistical control of error rates. We anticipate that this method could provide a powerful tool to explore the serum glycoproteome.

Primary Structure of Glycans by NMR Spectroscopy

Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

Diversity Matters: Optimal Collision Energies for Tandem Mass Spectrometric Analysis of a Large Set of N-Glycopeptides

Identification and characterization of N-glycopeptides from complex samples are usually based on tandem mass spectrometric measurements. Experimental settings, especially the collision energy selection method, fundamentally influence the obtained fragmentation pattern and hence the confidence of the database search results ("score"). Using standards of naturally occurring glycoproteins, we mapped the Byonic and pGlyco search engine scores of almost 200 individual N-glycopeptides as a function of collision energy settings on a quadrupole time of flight instrument. The resulting unprecedented amount of peptide-level information on such a large and diverse set of N-glycopeptides revealed that the peptide sequence heavily influences the energy for the highest score on top of an expected general linear trend with m/z. Search engine dependence may also be noteworthy. Based on the trends, we designed an experimental method and tested it on HeLa, blood plasma, and monoclonal antibody samples. As compared to the literature, these notably lower collision energies in our workflow led to 10-50% more identified N-glycopeptides, with higher scores. We recommend a simple approach based on a small set of reference N-glycopeptides easily accessible from glycoprotein standards to ease the precise determination of optimal methods on other instruments. Data sets can be accessed via the MassIVE repository (MSV000089657 and MSV000090218).

Proteomics and Biochemical Analyses of Secreted Proteins Revealed a Novel Mechanism by Which ADAM12S Regulates the Migration of Gastric Cancer Cells

Gastric cancer is one of the cancers with the highest morbidity and mortality. Although several therapeutic approaches have been developed to treat this disease, the overall survival rate is still very low due to metastasis, drug resistance, and so forth. Therefore, it is necessary to discover new regulatory molecules and signaling pathways that modulate the metastasis of gastric cancer cells. A Disintegrin And Metalloprotease 12 (ADAM12) was highly expressed in gastric cancer tissues and presented in the patient urine. However, it is unclear whether and how ADAM12 regulates the migration of gastric cancer cells. In this work, we used the secretome protein enrichment with click sugars (SPECS) method to purify the secreted glycosylated proteins and performed quantitative proteomics to identify the secreted proteins that were differentially regulated by ADAM12S, the short and secreted form of ADAM12. Our proteomic and biochemical analyses revealed that ADAM12S upregulated the cell surface glycoprotein CD146, a cell adhesion molecule and melanoma marker, which was dependent on the catalytic residue of ADAM12S. Furthermore, we discovered that the ADAM12S-enhanced migration of gastric cancer cells was, at least partially, mediated by CD146. This work may help to evaluate whether ADAM12 could be a potential therapeutic target for the treatment of gastric cancer patients.

Biochemical and ligand binding properties of recombinant Xenopus laevis cortical granule lectin-1

Intelectins are putative innate immune lectins that are found throughout chordates. The first intelectin reported was Xenopus laevis cortical granule lectin-1 (XCGL-1 or XL-35). XCGL-1 is critical in fertilization membrane development in Xenopus. Here, we explored the biochemical properties of XCGL-1. The cysteines responsible for forming intermolecular disulfide bonds were identified. XCGL-1 adopted a four-lobed structure as observed by electron microscopy. The full-length XCGL-1 and the carbohydrate recognition domain (CRD) bind galactose-containing carbohydrates at nanomolar to micromolar affinities. Molecular modeling suggested that galactoside ligands coordinated the binding site calcium ion and interacted with residues around the groove made available by the non-conserved substitution compared to human intelectin-1. Folding conditions for production of recombinant XCGL-1 CRD were also investigated. Our results not only provide new biochemical insights into the function of XCGL-1, but may also provide foundation for further applications of XCGL-1 as glycobiology tools.

Qualitative and quantitative mass spectrometry comparison of characteristic galactosyl lactose isomers from goat milk at different lactation stages

Galactooligosaccharides are composed mainly of galactosyl lactose, which is important for infant growth and as a functional food additive. Although galactosyl lactose is abundant in goat milk, its complex structure has hindered the separation and analysis of its isomers. In this study, 5 isomers of goat milk galactosyl lactose were separated by HPLC: β6'-galactosyl lactose (β6'-GL), α6'-galactosyl lactose (α6'-GL), β4'-galactosyl lactose (β4'-GL), α3'-galactosyl lactose (α3'-GL), and β3'-galactosyl lactose (β3'-GL). This composition differs from that of commercial galactooligosaccharide products, which comprise mainly β-configuration oligosaccharides. The isomers were then qualitatively and quantitatively compared at different lactation stages using online HPLC-mass spectrometry. Relative quantitative analysis showed that the total content of the 5 galactosyl lactose isomers was highest in transitional goat milk. Specifically, β3'-GL was the main isomer in colostrum and α3'-GL was the main isomer in transitional and mature milk. β6'-Galactosyl lactose and β4'-GL tended to increase and then decrease during lactation. Moreover, α3'-GL content was 2 times higher than in colostrum and 10 times higher in transitional milk than in mature milk; in contrast, for β3'-GL, the values were 5 and 2 times higher, respectively. Absolute quantitative analysis revealed that β3'-GL was the most abundant isomers in colostrum (32.3 mg/L), and α3'-GL was the most abundant in transitional milk (88.1 mg/L) and mature milk (36.3 mg/L). These findings provide an important quantitative basis for understanding the relationship between structure and function of galactosyl lactose in goat milk, as well as its exploitation as a functional food.

Integrated Chemoenzymatic Approach to Streamline the Assembly of Complex Glycopeptides in the Liquid Phase

Glycosylation of proteins is a complicated post-translational modification. Despite the significant progress in glycoproteomics, accurate functions of glycoproteins are still ambiguous owing to the difficulty in obtaining homogeneous glycopeptides or glycoproteins. Here, we describe a streamlined chemoenzymatic method to prepare complex glycopeptides by integrating hydrophobic tag-supported chemical synthesis and enzymatic glycosylations. The hydrophobic tag is utilized to facilitate peptide chain elongation in the liquid phase and expeditious product separation. After removal of the tag, a series of glycans are installed on the peptides via efficient glycosyltransferase-catalyzed reactions. The general applicability and robustness of this approach are exemplified by efficient preparation of 16 well-defined SARS-CoV-2 O-glycopeptides, 4 complex MUC1 glycopeptides, and a 31-mer glycosylated glucagon-like peptide-1. Our developed approach will open up a new range of easy access to various complex glycopeptides of biological importance.

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.

High-Resolution Native Mass Spectrometry

Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.

Molecularly imprinted polymers outperform lectin counterparts and enable more precise cancer diagnosis

Accurately analysing the particular glycosylation status of protein biomarkers is of significant importance in the precise, early diagnosis of cancer. Existing methods mainly rely on the use of antibodies and lectins. However, due to the macroscopic and microscopic heterogeneity of glycans, precise analysis of glycosylation status still remains a challenge. Molecularly imprinted polymers (MIPs), as a synthetic alternative to antibodies or lectins, may provide new solutions but have not yet been explored. Herein, we report an appealing strategy called triple MIP-based plasmonic immunosandwich assay (triMIP-PISA) for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers. As proof of the principle, alpha fetoprotein (AFP), which has been used as a clinical biomarker for early detection of hepatocellular carcinoma (HCC), as well as its Lens culinaris agglutinin (LCA)-reactive fraction (AFP-L3), which is mainly composed of core-fucosylated glycans, were used as two target proteoforms to test in this study. Using two MIPs that can specifically recognize the peptide sequence of AFP as well as a fucose-imprinted MIP that can specifically recognize the AFP-L3 fraction, facile simultaneous plasmon-enhanced Raman detection of AFP and AFP-L3 in serum was achieved, which allowed HCC patients to be distinguished from healthy individuals. Due to the excellent recognition properties of the MIPs that are comparable to those of antibodies and superior to those of lectins, our triMIP-PISA method exhibited improved precision as compared with an antibody plus lectin-based immunofluorescence assay. Thus, this strategy opened a new avenue towards the precise diagnosis of cancer.

Single Molecule-Level Detection via Liposome-Based Signal Amplification Mass Spectrometry Counting Assay

Because of the low atomization and/or ionization efficiencies of many biological macromolecules, the application of mass spectrometry to the direct quantitative detection of low-abundance proteins and nucleic acids remains a significant challenge. Herein, we report mass spectrum tags (MS-tags) based upon gold nanoparticle (AuNP)-templated phosphatidylcholine phospholipid (DSPC) liposomes, which exhibit high and reliable signals via electrospray ionization (ESI). Using these MS-tags, we constructed a liposome signal amplification-based mass spectrometric (LSAMS) "digital" counting assay to enable ultrasensitive detection of target nucleic acids. The LSAMS system consists of liposomes modified with a gold nanoparticle core and surface-anchored photocleavable DNA. In the presence of target nucleic acids, the modified liposome and a magnetic bead simultaneously hybridize with the target nucleic acid. After magnetic separation and photolysis, the MS-tag is released and can be analyzed by ESI-MS. At very low target concentrations, one liposome particle corresponds to one target molecule; thus, the concentration of the target can be estimated by counting the number of liposomes. With this assay, hepatitis C (HCV) virus RNA was successfully analyzed in clinical samples.

Glycan and Protein Analysis of Glycoengineered Bacterial E. coli Vaccines by MALDI-in-Source Decay FT-ICR Mass Spectrometry

Bacterial glycoconjugate vaccines have a major role in preventing microbial infections. Immunogenic bacterial glycans, such as O-antigen polysaccharides, can be recombinantly expressed and combined with specific carrier proteins to produce effective vaccines. O-Antigen polysaccharides are typically polydisperse, and carrier proteins can have multiple glycosylation sites. Consequently, recombinant glycoconjugate vaccines have a high structural heterogeneity, making their characterization challenging. Since development and quality control processes rely on such characterization, novel strategies are needed for faster and informative analysis. Here, we present a novel approach employing minimal sample preparation and ultrahigh-resolution mass spectrometry analysis for protein terminal sequencing and characterization of the oligosaccharide repeat units of bacterial glycoconjugate vaccines. Three glycoconjugate vaccine candidates, obtained from the bioconjugation of the O-antigen polysaccharides from E. coli serotypes O2, O6A, and O25B with the genetically detoxified exotoxin A from Pseudomonas aeruginosa, were analyzed by MALDI-in-source decay (ISD) FT-ICR MS. Protein and glycan ISD fragment ions were selectively detected using 1,5-diaminonaphtalene and a 2,5-dihydroxybenzoic acid/2-hydroxy-5-methoxybenzoic acid mixture (super-DHB) as a MALDI matrix, respectively. The analysis of protein fragments required the absence of salts in the samples, while the presence of salt was key for the detection of sodiated glycan fragments. MS/MS analysis of O-antigen ISD fragments allowed for the detection of specific repeat unit signatures. The developed strategy requires minute sample amounts, avoids the use of chemical derivatizations, and comes with minimal hands-on time allowing for fast corroboration of key structural features of bacterial glycoconjugate vaccines during early- and late-stage development.

Identification and quantification of sialylated and core-fucosylated N-glycans in human transferrin by UPLC and LC-MS/MS

Sialylated and core-fucosylated N-glycans in human transferrin (HTF) are used as glycan biomarkers due to their increased or decreased characteristics in certain diseases. However, their absolute quantities remain unclear. In this study, N-glycans of HTF were identified by UPLC and LC-MS/MS using fluorescence tags [2-aminobenzamide (AB) and procainamide (ProA)] and columns [HILIC and anion exchange chromatography-HILIC (AXH)]. The structures of 14 (including five core-fucosylated) N-glycans in total comprising two non-, six mono-, four di-, and two tri-sialylated N-glycans were identified. The quantities (%) of each N-glycan relative to the total N-glycans (100%) were obtained. HILIC and AXH were better for peak identification and separability except for desialylation, respectively. Specifically, sialylated (in ProA-HILIC and ProA-AXH by UPLC or LC-MS/MS) and core-fucosylated (in AB-HILIC and ProA-AXH by UPLC) N-glycans were efficiently identified. Seven neuraminidase-treated (including three core-fucosylated) N-glycans were efficiently identified in ProA-AXH, even their poor separation. Additionally, ProA-AXH was more efficient for the estimation of the absolute quantities of N-glycans from the results of fluorescence intensity (by UPLC) and relative quantity (by LC-MS/MS). These results first demonstrate that ProA is useful for identifying and quantifying sialylated, core-fucosylated, and neuraminidase-treated desialylated N-glycans in HTF using AXH by UPLC and LC/MS.

Comparative analysis of yak milk and bovine milk glycoprotein N/O-glycome by online HILIC-UV-ESI-MS/MS

Yak milk (YM) has higher protein content than other bovine milk (BM) varieties. The bioactivity of milk glycoproteins is related to N/O-glycans. We qualitatively and quantitatively compared the N/O-glycome of YM and BM glycoproteins using stable isotope labeling combined with hydrophilic interaction chromatography and electrospray ionization mass spectrometry. We identified 79 and 78 N-glycans in YM and BM, respectively. Two N-glycans (H4N5F1A1; H5N4F1) were exclusive to YM. The content ratios of different types of N-glycans differed significantly between YM and BM, with sialylated N-glycans 2.33 times more abundant in YM. Five and seven O-glycans were detected in YM and BM, respectively. Two O-glycans (H1N2; H1N2A1) were exclusive to BM. The bi-sialylated O-glycan, H1N1A2, accounted for 56.1% of O-glycans in YM; it was 5.97 times more abundant in YM than in BM (equal volume basis). This study provides a theoretical basis for the future utilization of YM as a functional food.

The antibody-binding Fc gamma receptor IIIa / CD16a is N-glycosylated with high occupancy at all five sites

The antibody-binding Fc γ receptors (FcγRs) trigger life-saving immune responses and many therapeutic monoclonal antibodies require FcγR engagement for full effect. One proven strategy to improve the efficacy of antibody therapies is to increase receptor binding affinity, in particular binding to FcγRIIIa/CD16a. Currently, affinities are measured using recombinantly-expressed soluble extracellular FcγR domains and CD16a-mediated antibody-dependent immune responses are characterized using cultured cells. It is notable that CD16a is highly processed with multiple N-glycosylation sites, and preventing individual N-glycan modifications affects affinity. Furthermore, multiple groups have demonstrated that CD16a N-glycan composition is variable and composition impacts antibody binding affinity. The level of N-glycosylation at each site is not known though computational prediction indicates low to moderate potential at each site based on primary sequence (40-70%). Here we quantify occupancy of the extracellular domains using complementary mass spectrometry-based methods. All five sites of the tighter-binding CD16a V158 allotype showed 65-100% N-glycan occupancy in proteomics-based experiments. These observations were confirmed using intact protein mass spectrometry that demonstrated the predominant species corresponded to CD16a V158 with five N-glycans, with a smaller contribution from CD16a with four N-glycans. Occupancy was likewise high for the membrane-bound receptor at all detected N-glycosylation sites using CD16a purified from cultured human natural killer cells. Occupancy of the N162 site, critical for antibody binding, appeared independent of N169 occupancy based on analysis of the T171A mutant protein. The weaker-binding CD16a F158 allotype showed higher occupancy of >93% at each site.

Mannose-binding analysis and biological application of pradimicins

Pradimicins (PRMs) are an exceptional family of natural products that specifically bind d-mannose (Man). In the past decade, their scientific significance has increased greatly, with the emergence of biological roles of Man-containing glycans. However, research into the use of PRMs has been severely limited by their inherent tendency to form water-insoluble aggregates. Recently, we have established a derivatization strategy to suppress PRM aggregation, providing an opportunity for practical application of PRMs in glycobiological research. This article first outlines the challenges in studying Man-binding mechanisms and structural modifications of PRMs, and then describes our approach to address them. We also present our recent attempts toward the development of PRM-based research tools.

Formation and fragmentation of doubly and triply charged ions in the negative ion spectra of neutral N-glycans from viral and other glycoproteins

Structural determination of N-glycans by mass spectrometry is ideally performed by negative ion collision-induced dissociation because the spectra are dominated by cross-ring fragments leading to ions that reveal structural details not available by many other methods. Most glycans form [M - H]- or [M + adduct]- ions but larger ones (above approx. m/z 2000) typically form doubly charged ions. Differences have been reported between the fragmentation of singly and doubly charged ions but a detailed comparison does not appear to have been reported. In addition to [M + adduct]- ions (this paper uses phosphate as the adduct) other doubly, triply, and quadruply charged ions of composition [Mn + (H2PO4)n]n- have been observed in mixtures of N-glycans released from viral and other glycoproteins. This paper explores the formation and fragmentation of these different types of multiply charged ions with particular reference to the presence of diagnostic fragments in the CID spectra and comments on how these ions can be used to characterize these glycans.

A ratiometric electrochemical sensor for the determination of exosomal glycoproteins

Abnormal glycosylation of exosomal proteins is related to many diseases. However, there is still a lack of convenient and easy methods for the determination of exosomal glycoproteins. In this work, a ratiometric electrochemical sensor based on the recognition of glycoproteins by boronic acid and core-shell nanoparticles of silica-silver (SiO₂@Ag) amplified signals was developed for the highly sensitive detection of exosomal glycoproteins. The CD63 aptamer-SiO₂-N-(2-((2-aminoethyl)disulfanyl)ethyl) ferrocene carboxamide (FcNHSSNH₂) probe was first connected to graphene oxide-cucurbit [7] (GO-CB [7]) modified GCE through host-guest recognition. The CD63 aptamer was employed for the specific capture of exosomes, and the FcNHSSNH₂ molecule was used as the internal reference signal of the sensor. The mercaptophenylboronic acid (MPBA) of MPBA-SiO₂@Ag probe was used for the identification of exosomes surface glycoproteins. SiO₂ nanoparticle has a large specific surface area, which can load a large amount of silver nanoparticles (AgNPs) for electrochemical signal amplification. The results were expressed as the current ratio of AgNPs and FcNHSSNH₂. The introduction of the internal reference molecule FcNHSSNH₂ could effectively reduce the measurement error caused by the different DNA density of the substrate, and further improve the sensitivity and accuracy of the detection. Under the optimal experimental conditions, this sensor allowed the sensitive detection of exosomal glycoproteins in the range of 4.2 × 10² to 4.2 × 10⁸ particles/μL with a limit of detection (LOD) of 368 particles/μL. Furthermore, the ratiometric electrochemical sensor could be employed for the detection of exosomal glycoproteins in human serum samples, which has a good clinical application prospect.

Hydrophilic arginine-functionalized mesoporous polydopamine-graphene oxide composites for glycopeptides analysis

Considering the importance of glycopeptides in the clinical diagnosis of cancer and some serious diseases, the identification of glycopeptides from complex biological samples has attracted considerable attention. Effective pre-enrichment before mass spectrometry analysis plays an important role. In this work, a kind of hydrophilic two-dimensional composites (denoted as GO@MPDA@Arg) based on mesoporous polydopamine-graphene oxide were used to selectively enrich glycopeptides in biological samples. The mesoporous polydopamine (MPDA) layer self-assembled with template Pluronic F127 provided more binding sites to load arginine, and bound arginine enhanced the hydrophilicity of the material. As a result, GO@MPDA@Arg composites exhibited excellent enrichment performance for glycopeptides, containing good selectivity (IgG digests : BSA digests = 1:50, molar ratio), low detection limit for IgG digests (10 fmol μL^-1), high loading capacity for IgG digests (200 μg mg^-1), and good size exclusion (IgG digests : IgG : BSA = 1:100:100, mass ratio). In addition, mouse brain tissue was selected as the actual biological sample to further study the enrichment effect of GO@MPDA@Arg composites. In three parallel experiments, a total of 401 glycopeptides belonging to 233 glycoproteins were enriched from 200 μg digestion of mouse brain extract. The enrichment results demonstrate that GO@MPDA@Arg composites have application potential for glycopeptides enrichment in protein post-translational modification research.

Recent Advances in Lectin-Based Affinity Sorbents for Protein Glycosylation Studies

Glycosylation is one of the most significant post-translational modifications occurring to proteins, since it affects some of their basic properties, such as their half-life or biological activity. The developments in analytical methodologies has greatly contributed to a more comprehensive understanding of the quantitative and qualitative characteristics of the glycosylation state of proteins. Despite those advances, the difficulty of a full characterization of glycosylation still remains, mainly due to the complexity of the glycoprotein and/or glycopeptide mixture especially when they are present in complex biological samples. For this reason, various techniques that allow a prior selective enrichment of exclusively glycosylated proteins or glycopeptides have been developed in the past and are coupled either on- or off- line with separation and detection methods. One of the most commonly implemented enrichment methods includes the use of lectin proteins immobilized on various solid supports. Lectins are a group of different, naturally occurring proteins that share a common characteristic, which concerns their affinity for specific sugar moieties of glycoproteins. This review presents the different formats and conditions for the use of lectins in affinity chromatography and in solid phase extraction, including their use in dispersive mode, along with the recent progress made on either commercial or home-made lectin-based affinity sorbents, which can lead to a fast and automated glycosylation analysis.

Glycoform analysis of intact erythropoietin by MALDI FT-ICR mass spectrometry

Recombinant human erythropoietin (EPO) is a complex therapeutic glycoprotein with three N- and one O-glycosylation sites. Glycosylation of EPO influences its safety and efficacy and is defined as a critical quality attribute. Thus, analytical methods for profiling EPO glycosylation are highly demanded. Owing to the complexity of the intact protein, information about EPO glycosylation is commonly derived from released glycan and glycopeptide analysis using mass spectrometry (MS). Alternatively, comprehensive insights into the glycoform heterogeneity of intact EPO are obtained using ESI MS-based methods with or without upfront separation of EPO glycoforms. MALDI MS, typically performed with TOF mass analyzers, has been also used for the analysis of intact EPO but, due to the poor glycoform resolution, has only provided limited glycoform information. Here, we present a MALDI FT-ICR MS method for the glycosylation profiling of intact EPO with improved glycoform resolution and without loss of sialic acid residues commonly observed in MALDI analysis. Three EPO variants were characterized in-depth and up to 199 glycoform compositions were assigned from the evaluation of doubly-charged ions, without any deconvolution of the mass spectra. Key glycosylation features such as sialylation, acetylation, and N-acetyllactosamine repeats were determined and found to agree with previously reported data obtained from orthogonal analyses. The developed method allowed for a fast and straightforward data acquisition and evaluation and can be potentially used for the high-throughput comparison of EPO samples throughout its manufacturing process.

Desalting Paper Spay Mass Spectrometry (DPS-MS) for Rapid Detection of Glycans and Glycoconjugates

The detection of glycans and glycoconjugates has gained increasing attention in biological fields. Traditional mass spectrometry (MS)-based methods for glycoconjugate analysis are challenged with poor intensity when dealing with complex biological samples. We developed a desalting paper spray mass spectrometry (DPS-MS) strategy to overcome the issue of signal suppression of carbohydrates in salted buffer. Glycans and glycoconjugates (i.e., glycopeptides, nucleotide sugars, etc.) in non-volatile buffer (e.g., Tris buffer) can be loaded on the paper substrate from which buffers can be removed by washing with ACN/H2O (90/10 v/v) solution. Glycans or glycoconjugates can then be eluted and spray ionized by adding ACN/H2O/formic acid (FA) (10/90/1 v/v/v) solvent and applying a high voltage (HV) to the paper substrate. This work also showed that DPS-MS is applicable for direct detection of intact glycopeptides and nucleotide sugars as well as determination of glycosylation profiling of antibody, such as NIST monoclonal antibody IgG (NISTmAb). NISTmAb was deglycosylated with PNGase F to release N-linked oligosaccharides. Twenty-six N-linked oligosaccharides were detected by DPS-MS within a 5-minute timeframe without the need for further enrichment or derivatization. This work demonstrates that DPS-MS allows fast and sensitive detection of glycans/oligosaccharides and glycosylated species in complex matrices and has great potential in bioanalysis.

Structural dynamics and vibrational feature of N-Acetyl-d-glucosamine in aqueous solution

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.

Preparation of core-shell microporous organic polymer-coated silica microspheres for chromatographic separation and N-glycopeptides enrichment

Through a "one-pot" strategy, a layer of microporous organic polymer was coated onto the surface of monodisperse amino-functionalized silica microsphere via amino-aldehyde condensation reaction with core-shell structure. The change in chemical structure of material before and after modification was determined by Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy. Due to existence of a large number of amino and aldehyde groups in microporous organic polymer shell, the water contact angle decreased from 56.8° (silica microspheres) to 34.7° (microporous organic polymer-coated silica microspheres). Based on these properties, microporous organic polymer-coated silica microspheres were employed as the stationary phase for capillary liquid chromatography and successfully offered baseline separation of polar small molecules. Additionally, the material could also be served as the sorbent of hydrophilic interaction chromatography to enrich glycopeptides from human serum digest. A total of 470 unique N-glycopeptides and 342 N-glycosylation sites mapped to 112 N-glycosylated proteins were unambiguously identified from 2 μL of human serum, exhibiting a promising application prospect of microporous organic polymer-coated silica microspheres in the pretreatment of proteomics samples.

Glycosylated biomarker sensors: advancements in prostate cancer diagnosis

Prostate cancer is currently diagnosed using the conventional gold standard methods using prostate-specific antigen (PSA) as the selective biomarker. However, lack of precision in PSA screening has resulted in needless biopsies and delays the treatment of potentially fatal prostate cancer. Thus, identification of glycans as novel biomarkers for the early detection of prostate cancer has attracted considerable attention due to their reliable diagnostic platform compared with the current PSA systems. Therefore, biosensing technologies that provide point-of-care diagnostics have demonstrated the ability to detect various analytes, including glycosylated micro- and macro-molecules, thereby enabling versatile detection methodologies. This highlight article discusses recent advances in the biosensor-based detection of prostate cancer glycan biomarkers and the innovative strategies for the conjugation of nanomaterials adapted to biosensing platforms. Finally, the article is concluded with prospects and challenges of prostate cancer biosensors and recommendations to overcome the issues associated with prostate cancer diagnosis.

Glycosylation and Cardiovascular Diseases

Cardiovascular disease (CVD) is the leading cause of death worldwide, accounting for approximately 18 million deaths in 2017. Coronary artery disease is the predominant cause of death from CVD, followed by stroke. Owing to recent technological advancements, glycans and glycosylation patterns of proteins have been investigated in association with CVD risk factors and clinical events. These studies have found significant associations of glycans as biomarkers of systemic inflammation and major CVD risk factors and events. While more limited, studies have also shown that glycans may be useful for monitoring response to anti-inflammatory therapies and may be responsive to changes in lifestyle, particularly in patients with chronic inflammatory diseases. Glycans capture summative risk information related to inflammatory, immune, and signaling pathways and are promising biomarkers for CVD risk prediction and therapeutic monitoring.

A novel ratiometric MALDI-MS quantitation strategy for alkaline phosphatase activity with a homogeneous reaction and a tunable dynamic range

A unique ratiometric MALDI-MS strategy is proposed for the convenient and reliable quantitation of alkaline phosphatase based on the homogeneous enzymatic cleavage of a coded phosphopeptide (CPP)-triggered double-signal output. The dynamic range can be tuned by simply adjusting the primary concentration of CPP. The proposed strategy is also capable of being challenged by real human serum, and thus it may offer a wonderful approach for the convenient identification and quantitation of various enzyme activities in clinical diagnosis.

[Recent advances in functionalized magnetic nanomaterials for glycoprotein and glycopeptide enrichment]

Protein glycosylation is among the most common and important post-translational modifications, and plays an important regulatory role in many biological processes, including signal transduction, protein translation, and immune response. Abnormal protein glycosylation is also associated with numerous diseases, suggesting that glycoproteins may offer an array of useful disease biomarkers. Mass spectrometry (MS) has become an important analytical tool in glycoproteomics. However, the low abundance and weak ionization efficiency of glycopeptides have hindered direct mass spectrometric analyses, which remain considerably challenging. Glycoprotein and glycopeptide enrichment from complex biological samples is an important step in glycoproteomics. Diverse methods have recently been developed for specific glycoprotein and glycopeptide enrichment, including hydrophilic interaction liquid chromatography (HILIC), lectin affinity chromatography, boronate affinity chromatography, and hydrazide functional affinity chromatography. A variety of enrichment materials designed for the above strategies have been developed to meet the requirement of enriching low abundance glycoproteins and glycopeptides in complex samples. Magnetic solid phase extraction (MSPE) is an efficient sample pretreatment technology that offers advantages of simple operation, low cost, and high extraction efficiency. Functionalized magnetic nanomaterials have been widely used as adsorbents in glycoproteome studies. Since magnetic adsorbent is a key factor in MSPE, in this review, the preparation of magnetic nanomaterials functionalized with sugars, ionic liquids, lectins, boronate affinity ligands, metal organic frameworks, and covalent organic frameworks, and their applications in glycoprotein and glycopeptide enrichment are summarized. These functional magnetic nanomaterials possess high specific surface area and a large number of active adsorption sites, allowing different enrichment mechanisms, including HILIC, lectin affinity chromatography, and boronate and hydrazide functional affinity chromatography. These functional magnetic nanomaterials are mainly used to enrich glycoproteins and glycopeptides in serum, plasma, cells, tissues, saliva and other biological samples. Nearly 90 papers published in the last decade from the Science Citation Index (SCI) and Chinese core journals have been cited in this paper. Finally, the development and prospects of magnetic nanomaterials in glycoprotein and glycopeptide enrichment are also discussed.

The Hitchhiker's guide to glycoproteomics

Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.

Development of a multifunctional neoglycoside auxiliary for applications in glycomics research

A novel, multifunctional, tetrazine-containing neoglycoside auxiliary has been synthesized in three steps and 28% overall yield. The oxyamine was conjugated with unprotected carbohydrates under aqueous conditions (pH = 4.7), with DMF as a cosolvent, to provide neoglycosides in yields ranging between 51% and 68%. This auxiliary displayed broad advantages in the isolation and purification of complex carbohydrate mixtures, compatibility during extension by glycosyltransferases, and direct conjugation to chemical probes. Furthermore, the auxiliary can be removed in 96% yield under acidic conditions (0.25% TFA in H2O) that leave glycosidic linkages intact. Thereby, the tetrazine-containing neoglycoside auxiliary can serve to facilitate future glycomics investigations.

Glycoprotein analysis using lectin microcolumns and capillary electrophoresis: Characterization of alpha1-acid glycoprotein by combined separation methods

Separations based on combinations of 2.1 mm I.D. high-performance affinity microcolumns and capillary electrophoresis were developed and used to characterize the glycoforms of an intact glycoprotein. Human alpha₁-acid glycoprotein (AGP) was used as a model analyte due to its heterogeneous glycosylation resulting from variations in its degree of branching, fucosylation, and number of sialic acids. Three separation formats were examined based on microcolumns that contained the lectins concanavalin A (Con A) or Aleuria aurantia lectin (AAL). These microcolumns were used with one another or in combination with capillary electrophoresis. N-Glycan analysis of the non-retained and retained AGP fractions was carried out by using PNGase F digestion and nanoflow electrospray ionization mass spectrometry. Con A microcolumns were found to selectively enrich AGP that contained bi-antennary N-glycans, while AAL microcolumns retained AGP with fucose-containing N-glycans. Results from these separation methods indicated that fucosylation of the N-linked glycans was more abundant when a high degree of branching was present in AGP. Sialic acid residues were more abundant when higher degrees of branching and more fucose residues were present in AGP. The separation and analysis methods that were developed could be used with relatively small amounts of AGP and can be adapted for use with other intact glycoproteins.

Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells

N-glycosylation of glycoproteins, a major post-translational modification, plays a crucial role in various biological phenomena. In central nervous systems, N-glycosylation is thought to be associated with differentiation and regeneration; however, the state and role of N-glycosylation in neuronal differentiation remain unclear. Here, we conducted sequential LC/MS/MS analyses of tryptic digest, enriched glycopeptides, and deglycosylated peptides of proteins derived from human-induced pluripotent stem cells (iPSCs) and iPSC-derived neuronal cells, which were used as a model of neuronal differentiation. We demonstrate that the production profiles of many glycoproteins and their glycoforms were altered during neuronal differentiation. Particularly, the levels of glycoproteins modified with an N-glycan, consisting of five N-acetylhexosamines, three hexoses, and a fucose (HN5H3F), increased in dopaminergic neuron-rich cells (DAs). The N-glycan was deduced to be a fucosylated and bisected biantennary glycan based on product ion spectra. Interestingly, the HN5H3F-modified proteins were predicted to be functionally involved in neural cell adhesion, axon guidance, and the semaphorin-plexin signaling pathway, and protein modifications were site-selective and DA-selective regardless of protein production levels. Our integrated method for glycoproteome analysis and resultant profiles of glycoproteins and their glycoforms provide valuable information for further understanding the role of N-glycosylation in neuronal differentiation and neural regeneration.

Effective Enrichment Strategy Using Boronic Acid-Functionalized Mesoporous Graphene-Silica Composites for Intact N- and O-Linked Glycopeptide Analysis in Human Serum

The heterogeneity and low abundance of protein glycosylation present challenging barriers to the analysis of intact glycopeptides, which is key to comprehensively understanding the role of glycosylation in an organism. Efficient and specific enrichment of intact glycopeptides could help greatly with this problem. Here, we propose a new enrichment strategy using a boronic acid (BA)-functionalized mesoporous graphene-silica composite (denoted as GO@mSiO₂-GLYMO-APB) for isolating intact glycopeptides from complex biological samples. The merits of this composite, including high surface area and synergistic effect from size exclusion functionality of mesoporous material, hydrophilic interaction of silica, and the reversible covalent binding with BA, enable the effective and specific enrichment of both intact N- and O-glycopeptides. The results from the enrichment performance of the strategy evaluated by standard glycoproteins and the application to global N- and O-glycosylation analyses in human serum indicate the robustness and potential of the strategy for intact glycopeptide analysis.

The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells

Chinese hamster ovary (CHO) cells are one of the most commonly used host cell lines used for the production human therapeutic proteins. Much research over the past two decades has focussed on improving the growth, titre and cell specific productivity of CHO cells and in turn lowering the costs associated with production of recombinant proteins. CHO cell engineering has become of particular interest in recent years following the publication of the CHO cell genome and the availability of data relating to the proteome, transcriptome and metabolome of CHO cells. However, data relating to the cellular post-translational modification (PTMs) which can affect the functionality of CHO cellular proteins has only begun to be presented in recent years. PTMs are important to many cellular processes and can further alter proteins by increasing the complexity of proteins and their interactions. In this review, we describe the research presented from CHO cells to date related on three of the most important PTMs; glycosylation, phosphorylation and ubiquitination.

Single-cell fucosylation breakdown: Switching fucose to europium

Fucosylation and its fucosidic linkage-specific motifs are believed to be essential to understand their distinct roles in cellular behavior, but their quantitative information has not yet been fully disclosed due to the requirements of ultra-sensitivity and selectivity. Herein, we report an approach that converts fucose (Fuc) to stable europium (Eu) isotopic mass signal on hard ionization inductively coupled plasma mass spectrometry (ICP-MS). Metabolically assembled azido-fucose on the cell surface allows us to tag them with an alkyne-customized Eu-crafted bacteriophage MS2 capsid nanoparticle for Eu signal multiplication, resulting in an ever lowest detection limit of 4.2 zmol Fuc. Quantitative breakdown of the linkage-specific fucosylation motifs in situ preserved on single cancerous HepG2 and paracancerous HL7702 cells can thus be realized on a single-cell ICP-MS platform, specifying their roles during the cancering process. This approach was further applied to the discrimination of normal hepatocellular cells and highly, moderately, and poorly differentiated hepatoma cells collected from real hepatocellular carcinoma tissues.

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Switching facile fucose to stable Eu mass signal on a single-cell ICP-MS platform

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Ever lowest LOD of 4.2 zmol FucAz was achieved using a Eu-decorated MS2 nanoparticle

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Single-cell breakdown of fucosidic linkage-specific motifs

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Discrimination of highly, moderately, and poorly differentiated HCC from normal ones