Duplex Stable Isotope Labeling (DuSIL) for Simultaneous Quantitation and Distinction of Sialylated and Neutral N-Glycans by MALDI-MS

O-GlycoIsoQuant: A Novel O-Glycome Quantitative Approach through Superbase Release and Isotopic Girard's P Labeling

Quantitative glycosylation analysis serves as an effective tool for detecting changes in glycosylation patterns in cancer and various diseases. However, compared with N-glycans, O-glycans present challenges in both qualitative and quantitative mass spectrometry analysis due to their low abundance, ease of peeling, lack of a universal enzyme, and difficult accessibility. To address this challenge, we developed O-GlycoIsoQuant, a novel O-glycome quantitative approach utilizing superbase release and isotopic Girard's P labeling. This method facilitates rapid and efficient nonreducing β-elimination to dissociate O-glycans from proteins using the organic superbase, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), combined with light and heavy isotopic Girard's reagent P (GP) labeling for relative quantification of O-glycans by mass spectrometry. Employing this method, labeled O-glycans exhibit a double peak with a mass difference of 5 Da, suitable for stable relative quantification. The O-GlycoIsoQuant method is characterized by its high labeling efficiency, excellent reproducibility (CV < 20%), and good linearity (R2 > 0.99), across a dynamic range spanning a 100-fold range. This method was applied to various complex sample types, including human serum, porcine spermatozoa, human saliva, and urinary extracellular vesicles, detecting 33, 39, 49, and 37 O-glycans, respectively, thereby demonstrating its broad applicability.

Serum N-glycomic profiling identifies candidate biomarker panels for assessing coronary artery stenosis severity

Stenosis severity may escalate over the course of coronary artery disease (CAD), increasing the risk of death for the patient. Conventionally, the assessment of stenosis degree relies on invasive coronary angiography (ICA), an invasive examination unsuitable for patients in poor physical condition or those with contrast allergies and one that imposes a psychological burden on patients. Although abnormal serum N-glycan profiles have exhibited robust associations with various cardiovascular diseases, including CAD, their potential in diagnosing CAD stenosis remains to be determined. In this study, we performed a comprehensive analysis of serum N-glycome from 132 patients who underwent ICA and 27 healthy controls using MALDI-TOF-mass spectrometry. The patients who underwent ICA examination were categorized into four groups based on stenosis severity: no/mild/moderate/severe stenosis. Twenty-seven N-glycans were directly quantified, and 47 derived glycan traits were obtained. Notably, among these 74 glycan features, 18 exhibited variations across the study groups. Using a combination of least absolute shrinkage and selection operator and logistic regression analyses, we developed five diagnostic models for recognizing stenosis degree. Our results suggested that alterations in serum N-glycosylation modifications might be valuable for identifying stenosis degree and monitoring disease progression in individuals with CAD. It is expected to offer a noninvasive alternative for those who could not undergo ICA because of various reasons. However, the diagnostic potential of serum N-glycan panels as biomarkers requires multicenter, large cohort validation in the future.

Advances in Mass Spectrometry-Based Blood Metabolomics Profiling for Non-Cancer Diseases: A Comprehensive Review

Blood metabolomics profiling using mass spectrometry has emerged as a powerful approach for investigating non-cancer diseases and understanding their underlying metabolic alterations. Blood, as a readily accessible physiological fluid, contains a diverse repertoire of metabolites derived from various physiological systems. Mass spectrometry offers a universal and precise analytical platform for the comprehensive analysis of blood metabolites, encompassing proteins, lipids, peptides, glycans, and immunoglobulins. In this comprehensive review, we present an overview of the research landscape in mass spectrometry-based blood metabolomics profiling. While the field of metabolomics research is primarily focused on cancer, this review specifically highlights studies related to non-cancer diseases, aiming to bring attention to valuable research that often remains overshadowed. Employing natural language processing methods, we processed 507 articles to provide insights into the application of metabolomic studies for specific diseases and physiological systems. The review encompasses a wide range of non-cancer diseases, with emphasis on cardiovascular disease, reproductive disease, diabetes, inflammation, and immunodeficiency states. By analyzing blood samples, researchers gain valuable insights into the metabolic perturbations associated with these diseases, potentially leading to the identification of novel biomarkers and the development of personalized therapeutic approaches. Furthermore, we provide a comprehensive overview of various mass spectrometry approaches utilized in blood metabolomics research, including GC-MS, LC-MS, and others discussing their advantages and limitations. To enhance the scope, we propose including recent review articles supporting the applicability of GC×GC-MS for metabolomics-based studies. This addition will contribute to a more exhaustive understanding of the available analytical techniques. The Integration of mass spectrometry-based blood profiling into clinical practice holds promise for improving disease diagnosis, treatment monitoring, and patient outcomes. By unraveling the complex metabolic alterations associated with non-cancer diseases, researchers and healthcare professionals can pave the way for precision medicine and personalized therapeutic interventions. Continuous advancements in mass spectrometry technology and data analysis methods will further enhance the potential of blood metabolomics profiling in non-cancer diseases, facilitating its translation from the laboratory to routine clinical application.

In-depth profiling of carbohydrate isomers in biological tissues by chemical derivatization-assisted mass spectrometry imaging

Carbohydrates play crucial regulatory roles in various physiological and pathological processes. However, the low ionization efficiency and the presence of linkage pattern, monosaccharide composition and anomeric configuration isomers make their in-depth analysis very challenging, especially for heterogeneous biological tissues. In this study, we propose a high-sensitive and isomer-specific imaging approach to visualize the spatial distributions of monosaccharide and disaccharide isomers by integrating chemical derivatization and matrix-assisted laser desorption/ionization tandem mass spectrometry imaging (MALDI-MS2I). 2-Pyridinecarbohydrazide (PYD) is developed as a novel derivatization reagent which can not only improves the MS sensitivity of carbohydrates, but also enables the identification and visualization of ketose and aldose monosaccharide isomers, as well as linkage pattern, monosaccharide composition and anomeric configuration disaccharide isomers by mass spectrometry imaging of isomer-specific MS/MS fragment ions. Moreover, we build quantitative MALDI-MS2 and MALDI-MS2I methods for disaccharide isomers based on the diagnostic fragment ions, and good linear relationships could be achieved both in solution and on glass slides. We expect that this study should provide new ideas for in-depth profiling of the spatial signatures of carbohydrates in biological tissues and lay the foundation for a deeper understanding of carbohydrates' structure.

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.

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.

Improved Glycoqueuing Strategy Reveals Novel α2,3-Linked Di-/Tri-Sialylated Oligosaccharide Isomers in Human Milk

Sialylated human milk oligosaccharides (SHMOs) possess unique biological activities. Qualitative and quantitative analyses of SHMOs at different lactation stages are limited by interference from neutral oligosaccharides, glycan structural complexity, and low detection sensitivity. Herein, our previously developed glycoqueuing strategy was improved and applied to enable an isomer-specific quantitative comparison of SHMOs between colostrum milk (CM) and mature milk (MM). A total of 49 putative structures were determined, including 1 α2,6-linked and 13 α2,3-linked isomers separated from seven newly discovered SHMO compositions. The content of most oligosaccharides was more than 50% lower in MM than in CM, and α2,3-sialylation was observed in 43.74% of SHMOs from CM and 22.95% of SHMOs from MM. Finally, the fucosylation level of the SHMOs increased from 16.45 to 22.28% with prolonged lactation. These findings provide the basis for further studies on the structure-activity relationship of SHMOs and a blueprint to improve infant formula.

Quantitative clinical glycomics strategies: A guide for selecting the best analysis approach

Glycans introduce complexity to the proteins to which they are attached. These modifications vary during the progression of many diseases; thus, they serve as potential biomarkers for disease diagnosis and prognosis. The immense structural diversity of glycans makes glycosylation analysis and quantitation difficult. Fortunately, recent advances in analytical techniques provide the opportunity to quantify even low-abundant glycopeptides and glycans derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Understanding the strengths and weaknesses of different quantitative glycomics analysis methods is important for selecting the best strategy to analyze glycosylation changes in any given set of clinical samples. To provide guidance towards selecting the proper approach, we discuss four widely used quantitative glycomics analysis platforms, including fluorescence-based analysis of released N-linked glycans and three different varieties of MS-based analysis: liquid chromatography (LC)-mass spectrometry (MS) analysis of glycopeptides, matrix-assisted laser desorption ionization-time of flight MS, and LC-ESI-MS analysis of released N-linked glycans. These methods' strengths and weaknesses are compared, particularly associated with the figures of merit that are important for clinical biomarker studies, including: the initial sample requirements, the methods' throughput, sample preparation time, the number of species identified, the methods' utility for isomer separation and structural characterization, method-related challenges associated with quantitation, repeatability, the expertise required, and the cost for each analysis. This review, therefore, provides unique guidance to researchers who endeavor to undertake a clinical glycomics analysis by offering insights on the available analysis technologies.

On-tissue derivatization for isomer-specific mass spectrometry imaging and relative quantification of monosaccharides in biological tissues

Spatially-resolved profiling of tissue monosaccharides not only gives an insight into the spatial heterogeneity of monosaccharides, but also helps to decipher the possible roles of monosaccharides in biological processes. Here, we develop an on-tissue derivatization method, coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to image and quantify the aldose and ketose isomers of monosaccharide in biological tissues. A new derivatization reagent, 1-naphthaleneacethydrazide (NAH) was synthesized for the on-tissue derivatization of monosaccharides, and it significantly enhanced the imaging sensitivity of monosaccharides. Moreover, the NAH-derivatized aldose and ketose can generate isomer-specific diagnostic ions during MALDI-MS/MS analysis, and thus paves way for the isomer-specific MS imaging of aldose and ketose monosaccharides. On this basis, we further constructed a quantitative MALDI-MS imaging model based on isomer-specific diagnostic ions, and calculated the expression contents of aldose and ketose monosaccharide isomers in different tissue regions of carrot section. We expect that the development of this method should provide more precise view on the spatial distributions and contents of different monosaccharides in heterogeneous biological tissues.

Relative quantitation of glycans in cetuximab using ultra-high-performance liquid chromatography-high-resolution mass spectrometry by Pronase E digestion

Glycans play important roles in the activity and function of monoclonal antibodies (mAbs). In this study, an isotope labeling method for the relative quantitative analysis of glycans in cetuximab, a chimeric human/mouse IgG1 monoclonal antibody that specifically targets epidermal growth factor receptor, via hydrophilic interaction LC-ultra-high-performance LC-HRMS was established based on Pronase E digestion. To this aim, novel isotope MS probes, i.e., 3-benzoyl-2-oxothiazolidine-4-carboxylic acid (d0-BOTC) and 3-(2,3,4,5,6-pentadeuterio-benzoyl)-2-oxothiazolidine-4-carboxylate acid (d5-BOTC), which include a carboxyl group to target the amino functional group in glycosylamine, were developed. The nonspecific Pronase E enzyme could simultaneously digest the peptide bound to the N- and O-glycans into glycosylamine having only one amino acid. Since the mass difference between the light- and heavy-labeled glycans was 5.0 Da, the relative abundance of their MS peaks was used to achieve the qualitative and relative quantitative analysis of glycans. Sialylglycopeptide was used as a complex glycan model to validate the accuracy of the method. The results demonstrated the good linearity (R² ≥ 0.9994) between the experimentally detected MS intensity ratios and the theoretical molar ratios of the d0-BOTC to the corresponding d5-BOTC derivatives in the dynamic range of 0.03-10 and 0.03-20 of three orders magnitude for the d5-BOTC/d0-BOTC ratios. The reproducibility was between 0.16% and 10.70%, and the limit of detection was 13 fmol. The feasibility of the relative quantification method was investigated by analyzing the glycan content in cetuximab, finding good consistency between experimental and theoretical molar ratios (5:1, 3:1, 1:1, 1:3, 1:5) of d0/d5-BOTC-labeled glycans. Finally, 13 glycans were successfully identified in cetuximab by applying this method using an in-house Tracefinder database. This study provides a novel strategy for the high throughput analysis, identification, and functional study of glycans in mAbs.

A dual-mode reactive matrix for sensitive and quantitative analysis of carbohydrates by MALDI-TOF MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely used tool for the analysis of carbohydrates. However, the detection of carbohydrates by MALDI-TOF MS is often limited by the unsatisfactory ionization efficiency, instability and the matrix interference in low molecular weight region. Here, we demonstrate that a reactive matrix, 2-hydrazinoquinoline (2-HQ), can be used to detect neutral, sialic and low molecular weight carbohydrates sensitively both in the positive and negative ion mode. Since 2-HQ reacts efficiently with the reducing end of carbohydrate to form stable hydrazone, the ionization efficiency of derived carbohydrates is significantly enhanced. Using 2-HQ, the sensitivity for analyzing glycans has been improved 10-fold and 100-fold compared with those using 3-aminquinoline (3-AQ) and 2,5-dihydroxybenzoic acid (DHB) as matrix, respectively. Moreover, quantitative analysis of neutral, acidic and low molecular weight carbohydrates has been achieved because of the good reproducibility by using 2-HQ as matrix. As a result, up to 50 glycans in a single sample spot of human fresh serum without any prior purification and enrichment have been successfully detected. Therefore, 2-HQ as a new reactive matrix has shown great potentials in widespread applications for sensitive, selective, quantitative, high speed and high throughput analysis of carbohydrates in complex samples by MALDI-TOF MS.

IgG N-glycans

Glycosylation, one of the most common post-translational modifications in mammalian cells, impacts many biological processes such as cell adhesion, proliferation and differentiation. As the most abundant glycoprotein in human serum, immunoglobulin G (IgG) plays a vital role in immune response and protection. There is a growing body of evidence suggests that IgG structure and function are modulated by attached glycans, especially N-glycans, and aberrant glycosylation is associated with disease states. In this chapter, we review IgG glycan repertoire and function, strategies for profiling IgG N-glycome and recent studies. Mass spectrometry (MS) based techniques are the most powerful tools for profiling IgG glycome. IgG glycans can be divided into high-mannose, biantennary complex and hybrid types, modified with mannosylation, core-fucosylation, galactosylation, bisecting GlcNAcylation, or sialylation. Glycosylation of IgG affects antibody half-life and their affinity and avidity for antigens, regulates crystallizable fragment (Fc) structure and Fcγ receptor signaling, as well as antibody effector function. Because of their critical roles, IgG N-glycans appear to be promising biomarkers for various disease states. Specific IgG glycosylation can convert a pro-inflammatory response to an anti-inflammatory activity. Accordingly, IgG glycoengineering provides a powerful approach to potentially develop effective drugs and treat disease. Based on the understanding of the functional role of IgG glycans, the development of vaccines with enhanced capacity and long-term protection are possible in the near future.

Deuterium Oxide Labeling for Global Omics Relative Quantification (DOLGOReQ): Application to Glycomics

A new relative quantification strategy for glycomics, named deuterium oxide (D₂O) labeling for global omics relative quantification (DOLGOReQ), has been developed based on the partial metabolic D₂O labeling, which induces a subtle change in the isotopic distribution of glycan ions. The relative abundance of unlabeled to D-labeled glycans was extracted from the overlapped isotopic envelope obtained from a mixture containing equal amounts of unlabeled and D-labeled glycans. The glycan quantification accuracy of DOLGOReQ was examined with mixtures of unlabeled and D-labeled HeLa glycans combined in varying ratios according to the number of cells present in the samples. The relative quantification of the glycans mixed in an equimolar ratio revealed that 92.4 and 97.8% of the DOLGOReQ results were within a 1.5- and 2-fold range of the predicted mixing ratio, respectively. Furthermore, the dynamic quantification range of DOLGOReQ was investigated with unlabeled and D-labeled HeLa glycans mixed in different ratios from 20:1 to 1:20. A good correlation (Pearson's r > 0.90) between the expected and measured quantification ratios over 2 orders of magnitude was observed for 87% of the quantified glycans. DOLGOReQ was also applied in the measurement of quantitative HeLa cell glycan changes that occur under normoxic and hypoxic conditions. Given that metabolic D₂O labeling can incorporate D into all types of glycans, DOLGOReQ has the potential as a universal quantification platform for large-scale comparative glycomic experiments.

One step carboxyl group isotopic labeling for quantitative analysis of intact N-glycopeptides by mass spectrometry

Here, we have developed an approach termed methylamine stable isotope labeling (MeSIL) to relatively quantify N-glycopeptides through one step labeling. It is the first time that this approach is applied to measure N-glycopeptide changes in huh7 cells after Zika virus infection and it has been revealed that differentially expressed N-glycopeptides played important roles in virus infection at the glycosylation site-specific level.

Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.

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.

Clinically Viable Assay for Monitoring Uromodulin Glycosylation

Uromodulin, also known as the Tamm-Horsfall protein or THP, is the most abundant protein excreted in human urine. It is associated with the progression of kidney diseases; therefore, changes in the glycosylation profile of this protein could serve as a potential biomarker for kidney health. The typical glycomics analysis approaches used to quantify uromodulin glycosylation involve time-consuming and tedious glycoprotein isolation and labeling steps, which limit their utility in clinical glycomics assays, where sample throughput is important. Herein, we introduce a radically simplified sample preparation workflow, with direct ESI-MS analysis, enabling the quantification of N-linked glycans that originate from uromodulin. The method omits any glycan labeling steps but includes steps to reduce the salt content of the samples, thereby minimizing ion suppression. The method is effective for quantifying subtle glycosylation differences of uromodulin samples derived from different biological states. As a proof of concept, glycosylation from samples that differ by pregnancy status were shown to be differentiable.

A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees

The nature of protein glycosylation renders cellular glycomics a very challenging task in having to deal with all the disparate glycans carried on membrane glycoproteins. Rapid mapping by mass spectrometry analysis provides only a coarse sketch of the glycomic complexity based primarily on glycosyl compositions, whereby the missing high-resolution structural details require a combination of multi-mode separations and multi-stages of induced fragmentation to gain sufficiently discriminative precision, often at the expenses of throughput and sensitivity. Given the available technology and foreseeable advances in the near future, homing in on resolving the terminal fucosylated, sialylated and/or sulfated structural units, or glycotopes, maybe a more pragmatic and ultimately more rewarding approach to gain insights into myriad biological processes mediated by these terminal coding units carried on important glycoproteins, to be decoded by a host of endogenous glycan-binding proteins and antibodies. A broad overview of recent technical advances and limitations in cellular glycomics is first provided as a backdrop to the propounded glycotope-centric approach based on advanced nanoLC-MS2/MS3 analysis of permethylated glycans. To prioritize analytical focus on the more tangible glycotopes is akin to first identifying the eye-catching and characteristic-defining flowers and fruits of the glyco-forest, to see the forest for the trees. It has the best prospects of attaining the much-needed balance in sensitivity, structural precision and analytical throughput to match advances in other omics.

GlycoHunter: An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans

Glycans are responsible for many biological activities; however, their structures are incredibly diverse and complex, often rendering the field of glycomics unsolvable by a single analytical technique. The development of multiple chemical derivatization strategies and bioinformatic software is responsible for some of the greatest analytical gains in the field of glycomics. The INLIGHT strategy is a chemical derivatization technique using hydrazide chemistry to derivatize the reducing end of N-linked glycans and incorporates either a natural (NAT, ¹²C₆) or a stable-isotope label (SIL, ¹³C₆) to carry out relative quantification. Here we present GlycoHunter, a user-friendly software created in MATLAB that enables researchers to accurately and efficiently process MS1 glycomics data where a NAT and SIL pair is generated for relative quantification, including but not limited to, INLIGHT. GlycoHunter accepts the commonly used data file formats imzML and mzXML and effectively identifies all peak pairs associated with NAT- and SIL-labeled N-linked glycans using MS1 data. It also includes the ability to tailor the search parameters and export the results for further analysis using Skyline or Excel.

Evaluation of prostate cancer based on MALDI-TOF MS fingerprinting of nanoparticle-treated serum proteins/peptides

The serum MALDI-TOF MS spectrum includes signals for serum proteins and peptides between 1000 and 12,000 Da in size, presenting a fingerprint-like pattern. However, whole serum MALDI-TOF MS signals are complex and prejudiced for data analysis. Pre-treatment with specific nanomaterials can simplify the mass spectrum while retaining the characteristics of the fingerprint pattern. In the present study, we used hydrophilic interaction chromatography nanoparticles (HICNPs) to enrich proteins and peptides in serum from a large number prostate cancer samples and controls. After pre-treatment with HICNPs, the serum MALDI-TOF MS signals for samples were simpler, with more analysable fingerprint-like patterns. Principal component analysis and partial least squares discriminant analysis of the samples demonstrated a significant difference in the MALDI-TOF signals between prostate cancer and controls, with an analytical accuracy of 77%, approaching that of methods based on prostate-specific antigen. Due to the low cost and high flux, MALDI-TOF MS fingerprinting can be used in large-scale evaluation of various cancers, including prostate cancer.

A preliminary study on isomer-specific quantification of sialylated N-glycans released from whey glycoproteins in human colostrum and mature milk using a glycoqueuing strategy

Sialylated N-glycans are an integral component of whey proteins in human milk and play an irreplaceable role in infant growth and development. Currently, there are few studies on quantitative comparison of sialylated N-glycans in milk obtained at different lactation stages. Here, a preliminary isomer-specific quantification of whey sialylated N-glycans of human colostrum milk (CM) and mature milk (MM) was performed by using our recently developed glycoqueuing strategy. Such a preliminary comparison revealed that the whey sialylated N-glycan content was 86.4% lower in MM than in CM. Twenty-three α2,6-linked sialylated N-glycan isomers were detected with no α2,3-linked isomer observed. For the first time, three mono-sialylated and four bi-sialylated glycan isomers were reported. With the prolongation of lactation, the relative abundance of mono-sialylated glycans increased, whilst the relative abundance of bi-sialylated glycans decreased significantly. These findings contribute to the understanding of the structure-function relationship of sialylated N-glycans in the human whey fraction.

Polydopamine-Modified TS-1 Zeolite Framework Nanoparticles as a Matrix for the Analysis of Small Molecules by MALDI-TOF MS

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using conventional organic matrices for detection of small molecules has some limitations, such as heterogeneous analyte/matrix co-crystals, as well as interference of matrices in the low-molecular-weight range. In this work, a zeolite framework nanomaterial, TS-1, was applied as a MALDI matrix for the analysis of small molecules by MALDI-MS for the first time. To improve the signal intensity and reproducibility, TS-1 was modified with polydopamine (TS-1@PDA). Using TS-1@PDA as a matrix, organic substances in the low-molecular-weight region such as amino acids, nucleosides, peptides, oligosaccharides, and fatty acids can be detected by MALDI-MS in positive ion mode. Compared with traditional organic matrices like 2,5-dihydroxybenzoic acid (2,5-DHB) and α-cyano-4-hydroxycinnamic acid (CHCA), TS-1@PDA has the advantages including the formation of uniform sample spots, small background interference at low molecular weight, and better salt tolerance. Furthermore, this matrix was employed for the analysis of endogenous glucose in urine samples, and the level of glucose was quantified with a linear range of 0-10 mM (R ² > 0.98). The results demonstrated that TS-1@PDA has the potential to be used as an effective MALDI matrix for the analysis of small molecules in biological samples with excellent reproducibility and moderate sensitivity.

N-Glycosylation of IgG and IgG-Like Recombinant Therapeutic Proteins: Why Is It Important and How Can We Control It?

Regulatory bodies worldwide consider N-glycosylation to be a critical quality attribute for immunoglobulin G (IgG) and IgG-like therapeutics. This consideration is due to the importance of posttranslational modifications in determining the efficacy, safety, and pharmacokinetic properties of biologics. Given its critical role in protein therapeutic production, we review N-glycosylation beginning with an overview of the myriad interactions of N-glycans with other biological factors. We examine the mechanism and drivers for N-glycosylation during biotherapeutic production and the several competing factors that impact glycan formation, including the abundance of precursor nucleotide sugars, transporters, glycosidases, glycosyltransferases, and process conditions. We explore the role of these factors with a focus on the analytical approaches used to characterize glycosylation and associated processes, followed by the current state of advanced glycosylation modeling techniques. This combination of disciplines allows for a deeper understanding of N-glycosylation and will lead to more rational glycan control.

Parallel On-Target Derivatization for Mass Calibration and Rapid Profiling of N-Glycans by MALDI-TOF MS

Glycosylation is an important post-translational modification of proteins, and abnormal glycosylation is involved in a variety of diseases. Accurate and rapid profiling of N-glycans by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is still technically challenging and hampered mainly by mass drift of instrument, manual identification of spectrum peaks, and poor cocrystallization with traditional matrices besides low ionization efficiency of analytes. In the present study, a parallel on-target derivatization strategy (POTDS), on the basis of two rationally combined matrices, i.e., 3-hydrazinobenzoic acid plus DHB (DHB/3HBA) and quinoline-3-carbohydrazide plus DHB (DHB/Q3CH), was proposed for mass calibration and rapid detection of reducing N-glycans. Both DHB/3HBA and DHB/Q3CH show high derivatization efficiency and can improve the ionization efficiency of reducing N-glycans significantly. For mass calibration, in combination with dextrans, DHB/3HBA and DHB/Q3CH prove to be highly sensitive matrices facilitating both MS and MS² calibration for N-glycans in dual polarities. For rapid identification, the regular mass difference observed for each N-glycan labeled with Q3CH and 3HBA respectively can eliminate the occurrence of false positives and promote automated identification of N-glycans in complex samples. For relative quantitation, the acid-base pair of DHB/Q3CH generates a concentrated cocrystallization of glycan-matrix mixtures at the edge of the droplet uniformly, exhibiting good linearity (R² > 0.998) and accuracy (RSD ≤ 10%). Furthermore, the established POTDS was successfully utilized to assess N-glycans of serum from HCC patients, revealing potential for biomarker discovery in clinical practice.

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.

Multiplex Quantitative Glycomics Enabled by Periodate Oxidation and Triplex Mass Defect Isobaric Multiplex Reagents for Carbonyl-Containing Compound Tags

Glycosylation is one of the most important post-translational modifications (PTMs) with essential physiological functions, including protein folding, cell signaling, and immune response. Thus, various qualitative and quantitative glycomics analysis strategies have been developed. Recently, the isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tag was developed for quantitative glycomics with multiplexing capacity and increased reporter ion yield. To further improve quantification efficiency and enable quantifying low-abundance species, the mass defect based triplex SUGAR (mdSUGAR) tag has been designed. In addition, we also introduce additional reaction sites for mdSUGAR at the terminal sialic acid by periodate oxidation of the polyhydroxy chain to extend the mass difference and lower the requirement for resolving power. As a result, mdSUGAR tags show complete labeling efficiency, improved fragmentation pattern, and accurate quantification. Moreover, the quantitative performance of the mdSUGAR tags in a complex system has been systematically evaluated and demonstrated reliable results.

Characterization of Cell Glycocalyx with Mass Spectrometry Methods

The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.

Glycoqueuing: Isomer-Specific Quantification for Sialylation-Focused Glycomics

Changes of α-2,3-/α-2,6-linked sialic acids (SAs) in sialylglycans have been found to be closely related with some diseases. However, accurate quantification of sialylglycans at the isomeric level remains challenging due to their instability, structural complexity, and low mass spectrometry (MS) detection sensitivity. Herein, we propose an analytical strategy named "glycoqueuing", which allows sequential chromatographic elution and high-sensitivity MS quantification of various sialylglycan isomers based on isotopic labeling followed by analysis via online reversed-phase high performance liquid chromatography coupling with MS (RP-HPLC-MS). The new method was validated by detailed structural identification and quantification of fetal bovine serum (FBS) N-linked sialylglycan isomers, during which many branching isomers were successfully differentiated, and 28 sialylglycan compositions with Neu5Gc residues were analyzed. The method was successfully applied to isomer-specific, quantitative comparison of sialylated N-glycans between bovine and rabbit immunoglobulin G (IgG) and the search for serum sialylated N-glycan biomarker candidates of hepatocellular carcinoma, during which a 55% increase of α-2,6-sialylated fucosylated N-glycans was revealed, demonstrating the great applicability and potential clinical usage of the method.

Providing Bionic Glycome as internal standards by glycan reducing and isotope labeling for reliable and simple quantitation of N-glycome based on MALDI- MS

Accurate, simple and economical methods for quantifying N-glycans are continuously required for discovering disease biomarkers and quality control of biopharmaceuticals. Quantitative N-glycomics based on MS using exogenous isotopic labeling internal standards is promising as it is simple and accurate. However, it is largely hampered by the lack of available glycan internal standard libraries with good coverage of the natural glycan structural heterogeneity as well as broad dynamic mass and ion abundance range. To overcome this limitation, we developed a novel method, providing 'Bionic Glycome' as internal standards for glycan quantitation by MALDI-MS. Bionic Glycome was produced using N-glycome from pooled samples to be analyzed as substrate by one step of glycan reducing and isotope labeling (Glycan-RAIL). Each bionic glycan has 3 Da mass increment over its corresponding glycan analyte based on hemiacetals/alditols and H/D mass difference. In addition, Bionic Glycome has the same glycome composition and similar glycome profile in abundance with N-glycome to be analyzed from biological sample. Through the investigation of single glycan standard and complex glycans released from model glycoprotein and serum, the results demonstrate that the method has good quantitative accuracy and high reproducibility. Lastly, this method was successfully used for discovery of lung cancer specific glycan markers by comparing the serum glycans from each sample in lung cancer group (n = 16) and healthy controls (n = 16), indicating its potential in clinical applications.

Quantitation of Neurotoxic Metabolites of the Kynurenine Pathway by Laser Desorption Ionization Mass Spectrometry (LDI-MS)

The metabolites of the mammalian kynurenine (KYN) pathway are generated from a branch of tryptophan metabolic pathway. The latter generates 3-hydroxykynurenine (3-HK), kynurenic acid (KYNA), quinolinic acid (QUIN), and picolinic acid (PIC) which are all strongly neuroactive, often with dramatically contrasting functional outcomes. Whereas KYNA and PIC are neuroprotective, 3-HK and QUIN are potently neurotoxic and attributed in major neurodegenerative diseases like schizophrenia, Alzheimer's disease, Huntington's disease, bipolar disorder, and depression. It is increasingly evident that the ratio(s) between the neurotoxic and neuroprotective metabolites may help predict the manifestations of disease vs. health. Therefore high-throughput platforms for determining the relative levels of these kynurenine metabolites in biofluids offer considerable potential. Current analytical tools for studying KYN pathway include assays of branching enzymes, PCR, immunoanalysis, and LCMS. None of these offer high-throughput, cost-effective analyses suited for clinical or drug-screening applications. In this report a laser desorption ionization mass spectrometry (LDI-MS) method is described using SBA-15 mesoporous silica. The system allows fast, high-resolution quantitation of neurotoxic kynurenines using targeted metabolomics on conventional MALDI platforms.