Glycan reductive isotope-coded amino acid labeling (GRIAL) for mass spectrometry-based quantitative N-glycomics

Unlocking the future of colorectal cancer detection: Advances in screening glycosylation-based biomarkers on biological mass spectrometry technology

The incidence of colorectal cancer (CRC) is increasingly affecting younger populations, with its mortality rate rising annually. However, current clinical diagnostic techniques, such as colonoscopy and CEA antigen testing, remain invasive and prone to false-positive results, complicating early diagnosis and intervention. Glycosylation, a key post-translational modification, plays an essential role in cellular function, physiological regulation, and disease processes. In recent years, mass spectrometry technology has emerged as a powerful tool for screening glycan biomarkers, owing to its exceptional separation capabilities and sensitivity. This review encompasses the advancements in CRC glycan biomarkers from 2016 to 2024, with particular emphasis placed on N/O-glycan biomarkers identified through mass spectrometry. Nonetheless, the intrinsic low abundance and polyhydroxy nature of glycans hinder the specificity and sensitivity of current glycan biomarkers. To overcome these limitations, this article outlines pretreatment strategies for N/O-glycans, including glycan release, enrichment, purification, and derivatization, in conjunction with relative quantification techniques and high-throughput bioinformatics tools for biomarker screening. These strategies are anticipated to enhance the efficiency and precision of glycan biomarker identification through mass spectrometry. These advancements hold significant promise for enhancing CRC prevention, diagnosis, and treatment, thereby potentially improving patient outcomes and quality of life.

4-Hydrazinoquinazoline acting as a reactive matrix for the rapid and sensitive analysis of neutral and sialylated glycans using MALDI MS

The direct analysis of glycans by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) presents limited sensitivity due to the lower ionization efficiency of glycans. Various chemical derivatization methods have been developed to improve the detection sensitivity of glycans, but most of them need tedious preparation and cleanup procedures. Herein, a reactive matrix, 4-hydrazinoquinazoline (4-HQ), was developed for the rapid and sensitive detection of both neutral and sialylated glycans by MALDI MS. With 4-HQ as the reactive matrix, the detection limits of maltoheptaose and A3 glycan decreased 100-fold and 20-fold, respectively, compared with the conventional matrix. Moreover, 4-HQ formed homogeneous crystals and therefore showed good shot-to-shot reproducibility. Finally, the reactive matrix was successfully applied for the analysis of glycans released from glycoproteins and human serum. Importantly, the application of 4-HQ is the same as that of a conventional matrix with the additional advantage of on-target reaction at room temperature. Thus, 4-HQ can be used for the routine analysis of glycans by MALDI MS due to its simple use, great reproducibility, and enhanced detection of both neutral and sialylated glycans.

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.

gQuant, an Automated Tool for Quantitative Glycomic Data Analysis

MALDI-MS-based glycan isotope labeling methods have been effectively and widely used for quantitative glycomics. However, interpretation of the data produced by MALDI-MS is inaccurate and tedious because the bioinformatic tools are inadequate. In this work, we present gQuant, an automated tool for MALDI-MS-based glycan isotope labeling data processing. gQuant was designed with a set of dedicated algorithms to improve the efficiency, accuracy and convenience of quantitation data processing. When tested on the reference data set, gQuant showed a fast processing speed, as it was able to search the glycan data of model glycoproteins in a few minutes and reported more results than the manual analysis did. The reported quantitation ratios matched well with the experimental glycan mixture ratios ranging from 1:10 to 10:1. In addition, gQuant is fully open-source and is coded in Python, which is supported by most operating systems, and it has a user-friendly interface. gQuant can be easily adapted by users for specific experimental designs, such as specific glycan databases, different derivatization types and relative quantitation designs and can thus facilitate fast glycomic quantitation for clinical sample analysis using MALDI-MS-based stable isotope labeling.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to 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, matrices, derivatization, MALDI imaging, fragmentation and 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. Much of this material is 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 the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

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.

8-plex LC-MS/MS Analysis of Permethylated N-Glycans Achieved by Using Stable Isotopic Iodomethane

Glycosylation is an important post-translational modification of proteins. Many diseases, such as cancer, have proved to be related to aberrant glycosylation. High throughput quantitative methods have gained attention recently in the study of glycomics. With the development of high-resolution mass spectrometry, the sensitivity of detection in glycomics has largely improved; however, most of the commonly used MS-based techniques are focused on relative quantitative analysis, which can hardly provide direct comparative glycomic quantitation results. In this study, we developed a novel multiplex glycomic analysis method on an LC-ESI-MS platform. Reduced glycans were stable isotopic labeled during the permethylation procedure, with the use of iodomethane reagents CH2DI, CHD2I, CD3I, 13CH3I, 13CH2DI, 13CHD2I, 13CD3I, and CH3I. Up to 8-plex glycomic profiling was possible in a single analysis by LC-MS, and a 100 k mass resolution was sufficient to allow a baseline resolution of the mass differences among the 8-plex labeled glycans. The major advantages of this method are that it overcomes quantitative fluctuations caused by nanoESI, it facilitates a level of comparative quantitative glycomic analysis that accurately reflects the quantitative information in samples, and it dramatically shortens analysis time. Quantitation validation was tested on glycans released from bovine fetuin and model glycoprotein mixtures (RNase B, bovine fetuin, and IgG) with good linearity (R2 = 0.9884) and a dynamic range from 0.1 to 10. The 8-plex strategy was successfully applied to a comparative glycomic study of cancer cell lines. The results demonstrate that different distributions of sialylated glycans are related to the metastatic properties of cell lines and provide important clues for a better understanding of breast cancer brain metastasis.

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.

Quantitative glycomics using liquid phase separations coupled to mass spectrometry

Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.

Isobaric Labeling of Intact Gangliosides toward Multiplexed LC-MS/MS-Based Quantitative Analysis

Gangliosides are sialic acid-containing glycosphingolipids recognized to play essential role in biological processes. Both the glycan and lipid structures influence their biological function and thus necessitate their determination as intact molecular species. To our knowledge, no multiplexed method for intact gangliosides currently exists. In this paper, we aimed to demonstrate an approach for isobaric labeling of intact gangliosides. Specifically, we carried out the rapid, chemoselective oxidation of sialic acid side chain in common ganglioside core structures using NaIO₄ followed by ligation with a carbonyl-reactive isobaric tandem mass tag (TMT) reagent and subsequent RPLC-MS/MS analysis. Attachment of the isobaric label was observed to improve the ionization efficiency of complex gangliosides using electrospray ionization. Fragmentation of the resulting [M + 2H]²⁺ ions of TMT-labeled gangliosides provided information-rich spectra containing fragments from the glycan, lipid, and TMT reporter ions. This facile approach enabled simultaneous quantification of up to six samples as well as identification of glycan and lipid compositions in a single injection. As a proof-of-concept, using porcine brain total ganglioside extracts pooled at known ratios, we obtained overall sample-to-sample precision of <12% RSD and mean error of <10%. This showcased the great promise and feasibility of this strategy for high-throughput analysis of intact gangliosides in biological extracts.

Metallic Element Chelated Tag Labeling (MeCTL) for Quantitation of N-Glycans in MALDI-MS

N-glycosylation plays an important role in chief biological and pathological processes. Quantifying the N-glycan is important since glycan alterations are related to many diseases. In this study, we developed a novel N-glycan quantitation approach using metallic element chelated tag labeling (MeCTL) through reductive amination. The MeCTL strategy is of high labeling efficiency and accurate in quantitation with high reproducibility (CV < 17.03%) and good linearity (R² > 0.99) within 2 orders of magnitude of dynamic range. Additionally, it provides significant cross-ring fragmentation to distinguish N-glycan isomers. Furthermore, multiplex quantitation by chelation with several different rare earth elements can be achieved. At last, this strategy has been successfully used for evaluation of N-glycan changes in human serum associated with CRC, indicating its potential in clinical applications including disease N-glycome profiling and relative quantitation.

Recent advances in mass spectrometric analysis of glycoproteins

Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.

Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis

N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CV<15%) as well as high sensitivity (LOD at fmol level). At last, the proposed method was successfully applied in the profiling of N-glycome in human serum, in which a total of 31 N-glycan masses were identified.

Advancements in mass spectrometry-based glycoproteomics and glycomics

Protein N-glycosylation plays a crucial role in a considerable number of important biological processes. Research studies on glycoproteomes and glycomes have already characterized many glycoproteins and glycans associated with cell development, life cycle, and disease progression. Mass spectrometry (MS) is the most powerful tool for identifying biomolecules including glycoproteins and glycans, however, utilizing MS-based approaches to identify glycoproteomes and glycomes is challenging due to the technical difficulties associated with glycosylation analysis. In this review, we summarize the most recent developments in MS-based glycoproteomics and glycomics, including a discussion on the development of analytical methodologies and strategies used to explore the glycoproteome and glycome, as well as noteworthy biological discoveries made in glycoproteome and glycome research. This review places special emphasis on China, where scientists have made sizeable contributions to the literature, as advancements in glycoproteomics and glycomincs are occurring quite rapidly.

Hydrazino-s-triazine based labelling reagents for highly sensitive glycan analysis via liquid chromatography-electrospray mass spectrometry

Labelling strategy plays an important role in mass spectrometry (MS) based glycan analysis due to the high hydrophilicity and low ionization efficiency of glycans. Ten hydrazino-s-triazine based labelling reagents were synthesized under facile and controllable conditions for highly sensitive liquid chromatography-electrospray mass spectrometry glycan analysis in this work. Attached to N-glycans through non-reductive reactions, these new labelling reagents were evaluated in aspect of the differently enhanced glycan response to mass spectrometry. Three of the ten labelling reagents demonstrated to be reliable and remarkable for glycan analysis with satisfactory linearity and lowered limits of detection using maltoheptaose (DP7) as model. Furthermore, the most optimal labelling reagent was taken as an example for highly sensitive profiling of N-linked glycans both cleaved from chicken avidin and glycoproteins in human serum, indicating prospective availability for these labelling reagents in frontier of glycomics researches.

Hydrazinonicotinic acid derivatization for selective ionization and improved glycan structure characterization by MALDI-MS

Selective ionization and improved glycan structure characterization by MALDI-MS were achieved through derivatization of glycans by hydrazinonicotinic acid under different acid catalysis.

PNGase F-mediated incorporation of 18O into glycans for relative glycan quantitation

An enzymatic four ¹⁸O-labeling strategy based on PNGase F-catalyzed glycan ¹⁸O-labeling (PCGOL) developed in this work can be used for simultaneous quantification of glycans, non-glycopeptides and glycopeptides in a single workflow.