Advances in sample preparation strategies for MS-based qualitative and quantitative N-glycomics

Correlation Between N-Glycan GnGnXF3 and the Allergic Immune Response Against Juniperus ashei Pollen

BACKGROUND

Cupressaceae pollen increasingly causes respiratory allergies worldwide. Carbohydrates are abundant in extracts of these pollens, and the associated allergens are highly glycosylated. However, the contribution of saccharides to the allergenicity of these species remains unknown.

METHODS

Juniperus ashei pollen extract was deglycosylated and characterised using SDS-PAGE and immunoblotting. Additionally, N- and O-glycans were purified from the extract, identified, used as inhibitors in IgE-immunoblotting and further analysed via basophil activation tests. The interactions between IgE and J. ashei glycans were analysed using a glycan array. Purified Jun a 1 was treated with β-N-acetylglucosaminidase S and analysed using immunoblotting. The native pollen extract was used to immunise rabbits, and the IgG response was analysed using ELISA and glycan array.

RESULTS

Deglycosylation of J. ashei proteins abolished the interaction between IgE and allergens. This effect primarily depends on N-glycans. Purified N-glycans triggered basophil activation in some patients. A biantennary N-glycan with terminal GlcNAc, β-1,2 xylose and core α-1,3 fucose (GnGnXF3) was the most abundant glycan identified. The glycan array confirmed its interaction with IgE. The contribution of terminal N-acetylglucosamines (GlcNAc) to IgE-Jun a 1 interaction was validated. Moreover, effective immunisation of rabbits with the native extract confirmed the immunogenicity of their N-glycans.

CONCLUSIONS

The IgE-J. ashei allergen interaction is broadly controlled through N-glycans different from MUXF3. GnGnXF3 exerts an immunogenic effect in humans and rabbits; terminal GlcNAc residues influence its recognition by IgE. These discoveries reinforce the role of N-glycans in the allergic response to J. ashei.

Recent Advances in Labeling-Based Quantitative Glycomics: From High-Throughput Quantification to Structural Elucidation

Glycosylation, a crucial posttranslational modification (PTM), plays important roles in numerous biological processes and is linked to various diseases. Despite its significance, the structural complexity and diversity of glycans present significant challenges for mass spectrometry (MS)-based quantitative analysis. This review aims to provide an in-depth overview of recent advancements in labeling strategies for N-glycomics and O-glycomics, with a specific focus on enhancing the sensitivity, specificity, and throughput of MS analyses. We categorize these advancements into three major areas: (1) the development of isotopic/isobaric labeling techniques that significantly improve multiplexing capacity and throughput for glycan quantification; (2) novel methods that aid in the structural elucidation of complex glycans, particularly sialylated and fucosylated glycans; and (3) labeling techniques that enhance detection ionization efficiency, separation, and sensitivity for matrix-assisted laser desorption/ionization (MALDI)-MS and capillary electrophoresis (CE)-based glycan analysis. In addition, we highlight emerging trends in single-cell glycomics and bioinformatics tools that have the potential to revolutionize glycan quantification. These developments not only expand our understanding of glycan structures and functions but also open new avenues for biomarker discovery and therapeutic applications. Through detailed discussions of methodological advancements, this review underscores the critical role of derivatization methods in advancing glycan identification and quantification.

Fabrication of biosensor for the assessment of radon and lead levels in the blood

This study aimed to develop and test a biosensor for detecting radioactive radon gas and lead ions in blood samples collected from donors in Iraq. The biosensor was made up of aptamer, acetic acid, malachite green, and TRIS-HAC, and results were measured using a fluorescence spectrophotometer. This study found that 222Rn in the blood varied between individuals, with higher levels in males and smokers, and the highest concentration found in a male patient with cancer. The biosensor used to detect 222Rn in the blood was effective, sensitive, and low-cost, and the levels detected were within the limits set by the WHO. The study also looked at pb+2, a toxic metal, and found that levels were within permissible limits. The biosensor was also effective in detecting pb+2. The correlations between the variables are generally weak to moderate, and there are some negative relationships between humidity and other variables. There are also some strong positive relationships between temperature (Tin) and temperature (Tout). The results suggest that these variables are not strongly correlated with each other, which is an important finding for understanding their potential effects on health outcomes. However, further validation and testing may be necessary before its widespread use in clinical settings. This study highlights the importance of monitoring these substances in the blood, especially for individuals with occupational exposure to radiation. The biosensor was found to be sensitive, cost-effective, fast to manufacture, and efficient compared to other detection devices. Therefore, the study recommends the use of this biosensor for measuring radon and lead ions in blood samples. The biosensor used in this study could be a useful tool for such monitoring.

Stable isotope labeling differential glycans discovery in the serum of acute myocardial infarction by ultrahigh-performance liquid chromatography-quadrupole-Orbitrap high resolution mass spectrometry

Acute myocardial infarction (AMI) poses a grave threat to human life. However, most clinical biomarkers have limitations of low sensitivity and specificity. Therefore, screening novel glycan biomarkers with high sensitivity and specificity is crucial for the prevention and treatment of AMI. The novel method of ultrahigh-performance liquid chromatography coupled to quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) with d0/d5-BOTC probe labeling for relative quantification of glycans based on Pronase E digestion was established to screen novel glycan biomarkers in the serum of 34 AMI patients relative to healthy volunteers. The monosaccharide model D-glucosamine was used to investigate the effectiveness of the derivatization; the limit of detection (S/N = 3) was 10 amol. The accuracy was verified based on the consistency of different theoretical molar ratios (d0/d5 = 1:2, 2:1) and intensity ratios following digestion of glycoprotein ribonuclease B. Expressions of H4N4F3SA, H4N6F2, H4N6SA, H4N6F3 and H5N4FSA in the serum were significantly different (p < 0.0005) between AMI patients and healthy volunteers. The area under the receiver operating characteristic curve (AUC) for H4N6SA, H5N4FSA, and H4N6F2 was greater than 0.9039. Based on the proposed method, H4N6SA, H5N4FSA, and H4N6F2 in human serum showed high accuracy and specificity and may serve as potential glycan biomarkers, crucial for the diagnosis and treatment monitoring of AMI.

2-Hydrazinoterephthalic Acid as a Novel Negative-Ion Matrix-Assisted Laser Desorption/Ionization Matrix for Qualitative and Quantitative Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Analysis of N-Glycans in Peach Allergy Research

Glycans recently attracted considerable attention as the proposal of cross-reactive carbohydrate determinants for food allergy. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is powerful in analyzing biomolecules, while its applications in glycans are still challenging. Herein, a novel reactive matrix-assisted laser desorption/ionization (MALDI) matrix, 2-hydrazinoterephthalic acid, was rationally designed and synthesized. It provides uniform co-crystallization with glycans and only produces deprotonated ions with high intensities in the negative-ion mode. In combination with sinapic acid, a rapid and high-throughput method was established for on-target analysis of glycans with a superior limit of detection at the femtomole level and a good linearity (R² > 0.999). Furthermore, the established method was successfully applied to quantify N-glycans in different cultivars and tissues of peach [Prunus persica (L.) Batsch]. Our work suggests the potential role of N-glycans as biomarkers for food-borne allergy and lays a methodological foundation for the elucidation of the possible relationship between carbohydrate epitopes and food allergy.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

An integrated stage-tip-based glycomic and glycoproteomic approach for simple and rapid N-glycosylation profiling of glycoproteins

Glycosylation is a post-translational modification that plays an active role in many cellular events. It also regulates many functions of proteins. Monoclonal antibody (mAb)-derived drugs are used to treat many diseases, and glycosylation affects the activity of such drugs developed. On the other hand, N-glycans may change in certain diseases. Therefore, rapid and efficient bioanalytical methods are needed for N-glycosylation profiling. The study aimed to develop an integrated stage-tip application for simple and rapid N-glycosylation profiling of glycoproteins. A fast and inexpensive N-glycosylation profiling was achieved by integrating all glycoproteomic and glycomic sample preparation steps into a stage-tip. The glycomic approach of the integrated stage-tip reduces the N-glycan profiling time from 2 days to approximately 2.5 hours. It also allows the profiling of immunoglobulin G (IgG) N-glycopeptides directly from human plasma. In addition, N-glycosylation profiling can be done in the developed method without sorbents C18 or others, such as strong-cation exchange (SCX) at the glycopeptide level.

Microfluidic Magnetic Analyte Delivery Technique for Separation, Enrichment, and Fluorescence Detection of Ultratrace Biomarkers

A microfluidic magnetic analyte delivery (μMAD) technique was developed to realize sample preparation and ultrasensitive biomarker detection. A simply designed microfluidic device was employed to carry out this technique, including a poly(dimethylsiloxane)-glass hybrid microchip having four straight rectangular channels and a permanent magnet. In the μMAD process, functionalized magnetic beads (MBs) were used to recognize and isolate analytes from a complex sample matrix, deliver analytes into tiny microchannels, and preconcentrate analytes in the magnetic trapping/detection region for in situ fluorescence detection. In the feasibility study and sensitivity optimization, horseradish peroxidase-labeled MBs were used, and critical parameters for the signal amplification performance of μMAD were carefully evaluated. At optimized conditions, a sensitivity improvement of at least 2 orders of magnitude was achieved. As a proof of concept, μMAD was combined with the enzyme-linked immunosorbent assay (ELISA), while carcinoembryonic antigen (CEA), prostate-specific antigen (PSA), and interleukin 6 (IL-6) were selected as model biomarkers. The limits of detection (LODs) of μMAD-ELISA were as low as 0.29 pg/mL for CEA, 0.047 pg/mL for PSA, and 0.021 pg/mL for IL-6, which corresponded to an over 200-fold reduction compared to their commercial ELISA results. Meanwhile, μMAD-ELISA revealed high selectivity and reproducibility. In clinical sample analysis, good accuracy was acquired for human serum analysis relative to commercial ELISA kits, and satisfied recoveries of 85.1-102% with RSDs of 1.7-9.8% for IL-6 and 84.7-113% with RSDs of 3.2-8.3% for interferon-γ were obtained. This ultrasensitive and easy operation technique provides a valuable approach for trace-level biomarker detection for practical applications.

Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis

Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.

Magnetic porous carbon-dependent platform for the determination of N-glycans from urine exosomes

A magnetic porous carbon-dependent platform is established to separate and determine N-glycans from urine exosomes of healthy people and patients with gastric cancer. The results of the comparison reveal that 6 N-glycans shared by the two groups are downregulated, most of which present core fucose or bisecting N-acetylglucosamine (GlcNAc) type. In addition, five shared N-glycans including two of sialic acid type are upregulated. These obvious differences indicate the close relationship between glycans and gastric cancer thus permitting early diagnosis. A magnetic porous carbon material (FeMPC) from MIL-101(Fe) was employed to separate and analyze N-glycans from urine exosomes of healthy people and patients with gastric cancer.

Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations

Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is now a well-developed method which allows for sample limited analysis. Specific fabrication of capillary columns is required for proper implementation and optimization when working in the nanoflow regime. Coupling the capillary column to the mass spectrometer for electrospray ionization (ESI) requires reduction of the subsequent emitter tip. Reduction of column diameter to capillary scale can produce improved chromatographic efficiency and the reduction of emitter tip size increased sensitivity of the electrospray process. This improved sensitivity and ionization efficiency is valuable in analysis of precious biological samples where analytes vary in size, ion affinity, and concentration. In this review we will discuss common approaches and challenges in implementing nLC-MS methods and how the advantages can be leveraged to investigate a wide range of biomolecules.

NEGATIVE ION MASS SPECTROMETRY FOR THE ANALYSIS OF N-LINKED GLYCANS

N-glycans from glycoproteins are complex, branched structures whose structural determination presents many analytical problems. Mass spectrometry, usually conducted in positive ion mode, often requires extensive sample manipulation, usually by derivatization such as permethylation, to provide the necessary structure-revealing fragment ions. The newer but, so far, lesser used negative ion techniques, on the contrary, provide a wealth of structural information not present in positive ion spectra that greatly simplify the analysis of these compounds and can usually be conducted without the need for derivatization. This review describes the use of negative ion mass spectrometry for the structural analysis of N-linked glycans and emphasises the many advantages that can be gained by this mode of operation. Biosynthesis and structures of the compounds are described followed by methods for release of the glycans from the protein. Methods for ionization are discussed with emphasis on matrix-assisted laser desorption/ionization (MALDI) and methods for producing negative ions from neutral compounds. Acidic glycans naturally give deprotonated species under most ionization conditions. Fragmentation of negative ions is discussed next with particular reference to those ions that are diagnostic for specific features such as the branching topology of the glycans and substitution positions of moieties such as fucose and sulfate, features that are often difficult to identify easily by conventional techniques such as positive ion fragmentation and exoglycosidase digestions. The advantages of negative over positive ions for this structural work are emphasised with an example of a series of glycans where all other methods failed to produce a structure. Fragmentation of derivatized glycans is discussed next, both with respect to derivatives at the reducing terminus of the molecules, and to methods for neutralization of the acidic groups on sialic acids to both stabilize them for MALDI analysis and to produce the diagnostic fragments seen with the neutral glycans. The use of ion mobility, combined with conventional mass spectrometry is described with emphasis on its use to extract clean glycan spectra both before and after fragmentation, to separate isomers and its use to extract additional information from separated fragment ions. A section on applications follows with examples of the identification of novel structures from lower organisms and tables listing the use of negative ions for structural identification of specific glycoproteins, glycans from viruses and uses in the biopharmaceutical industry and in medicine. The review concludes with a summary of the advantages and disadvantages of the technique. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Novel methods in glycomics: a 2019 update

Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.

Reverse capture for selectively and sensitively revealing the N-glycome of serum exosomes

Exosomes are emerging as a promising source of disease biomarkers. However, glycans from exosomes have been less studied. Here, for the first time, the N-glycome of human serum exosomes is reported and the potential of N-glycans from exosomes as a source for biomarker discovery is revealed.

Mass spectrometry-based qualitative and quantitative N-glycomics: An update of 2017-2018

N-glycosylation is one of the most frequently occurring protein post-translational modifications (PTMs) with broad cellular, physiological and pathological relevance. Mass spectrometry-based N-glycomics has become the state-of-the-art instrumental analytical pipeline for sensitive, high-throughput and comprehensive characterization of N-glycans and N-glycomes. Improvement and new development of methods in N-glycan release, enrichment, derivatization, isotopic labeling, separation, ionization, MS, tandem MS and informatics accompany side-by-side wider and deeper application. This review provides a comprehensive update of mass spectrometry-based qualitative and quantitative N-glycomics in the years of 2017-2018.

Separation methods hyphenated to mass spectrometry for the characterization of the protein glycosylation at the intact level

Glycosylation is one of the most common post-translational modifications of proteins that affects their biological activity, solubility, and half-life. Therefore, its characterization is of great interest in proteomic, particularly from a diagnostic and therapeutic point of view. However, the number and type of glycosylation sites, the degree of site occupancy and the different possible structures of glycans can lead to a very large number of isoforms for a given protein, called glycoforms. The identification of these glycoforms constitutes an important analytical challenge. Indeed, to attempt to characterize all of them, it is necessary to develop efficient separation methods associated with a sensitive and informative detection mode, such as mass spectrometry (MS). Most analytical methods are based on bottom-up proteomics, which consists in the analysis of the protein at the glycopeptides level after its digestion. Even if this approach provides essential information, including the localization and composition of glycans on the protein, it is also characterized by a loss of information on macro-heterogeneity, i.e. the nature of the glycans present on a given glycoform. The analysis of glycoforms at the intact level can overcome this disadvantage. The aim of this review is to detail the state-of-the art of separation methods that can be easily hyphenated with MS for the characterization of protein glycosylation at the intact level. The different electrophoretic and chromatographic approaches are discussed in detail. The miniaturization of these separation methods is also discussed with their potential applications. While the first studies focused on the development and optimization of the separation step to achieve high resolution between isoforms, the recent ones are much more application-oriented, such as clinical diagnosis, quality control, and glycoprotein monitoring in formulations or biological samples.

Efficient Mass Spectrometric Dissection of Glycans via Gold Nanoparticle-Assisted in-Source Cation Adduction Dissociation

Structural identification of glycans is important but remains challenging, for which tandem mass spectrometry has evolved as an indispensable tool. However, it requires additional complex hardware and extra time for ion extraction. Herein, we report a straightforward approach called gold nanoparticles (AuNPs)-assisted in-source cation adduction dissociation (isCAD) for efficient mass spectrometry (MS) dissection of glycans. Although AuNPs have been employed as an inorganic matrix for MALDI MS, this is the first report of AuNP-induced fragmentation. In this approach, AuNPs were employed as an energy absorber for laser ionization as well as a trigger for fragmentation, while residual or deliberately added sodium ions acted as a cationizing agent. The addition of sodium ions induced intensive fragmentation, but the addition of protons suppressed the fragmentation, allowing for facile tuning of the degree of fragmentation. In addition, it was found that larger oligosaccharides and glycans were much easier to fragment as compared with their smaller counterparts, and the use of high-concentration AuNPs effectively suppressed the degree of fragmentation and thereby provided abundant molecular ions. Without any extra hardware and ion extraction, this approach provides a straightforward, cost-efficient and tunable fragmentation for efficient MS dissection of saccharides, including monosaccharides, oligosaccharides, and glycans. Thus, it opens new access to efficient MS dissection of glycans.

Glycan analysis for protein therapeutics

Glycosylation can be a critical quality attribute for protein therapeutics due to its extensive impact on product safety and efficacy. Glycan characterization is important in the process of protein drug development, from early stage candidate selection to late stage regulatory submission. It is also an indispensable part in the evaluation of biosimilarity. This review discusses the effects of glycosylation on the stability and activity of protein therapeutics, regulatory considerations corresponding to manufacturing and structural characterization of glycosylated protein therapeutics, and focuses on mass spectrometry compatible separation methods for glycan characterization of protein therapeutics. These approaches include hydrophilic interaction liquid chromatography, reversed-phase liquid chromatography, capillary electrophoresis, porous graphitic carbon liquid chromatography and two-dimensional liquid chromatography. Advances and novelties in each separation method, as well as associated challenges and limitations, are discussed at the released glycan, glycopeptide, glycoprotein subunit and intact glycoprotein levels.